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Unimatrix Zero is a secluded place within the Borg collective where drones can be themselves while they regenerate, but only certain Borg have the ability to visit. The Borg Queen considers Unimatrix Zero a threat because she does not want her Borg to ever have traces of individuality, but Captain Janeway thinks it could give the Federation allies within the Collective. Janeway, Tuvok and B'Elanna Torres put Borg implants in their bodies and infiltrate the Borg Cube to try and free the select few that are able to go to Unimatrix Zero, giving them the ability to maintain their individuality outside of Unimatrix Zero. The away team has been injected with a neural suppressant to keep their Borg implants from really connecting them to the Collective.
While the away team is on the Borg Cube, Seven of Nine goes to Unimatrix Zero herself to tell the Borg within what the team is doing. Seven had been able to go there when she was part of the Collective and she still maintains that ability. In the past, she had a romantic relationship there with her fellow Borg, Axum, and when she meets him there again, she notices those feelings returning.
While the away team is headed for the Central Plexus of the Borg Cube, Tuvok notices that his neural suppressant is wearing off and the Borg Queen begins communicating with him telepathically. The Queen finally convinces Tuvok to stop Janeway and Torres as they download a virus to free the select group of drones. They manage to get the virus into the system, but Tuvok prevents them from leaving. More Borg drones appear and capture Captain Janeway, but Torres is able to get away. Tuvok restrains Janeway and puts her in contact with the queen.
The Borg Queen makes Janeway watch on a viewscreen as she blows up a different Borg Cube, destroying the thousands of lives on board, because she lost contact with three of the drones due to Janeway's virus. The Queen uses the virus Janeway used to free the drones and alters it to actually kill the drones. She tells Janeway that unless the captain tells the free drones to rejoin the collective, she will go to Unimatrix Zero and kill all of the drones inside. Janeway is put into contact with Chakotay on Voyager to tell him the free drones have to go back to the collective, but instead of telling him that directly, she secretly tells him to destroy Unimatrix Zero. Without Unimatrix Zero, the Queen will not be able to find all of the free drones, and if she destroys all of the Borg vessels they are on, she will destroy her entire fleet.
After Seven tells everybody in Unimatrix Zero of the plan, they all agree that it is the best way to handle the situation and they offer to help get the away team back to the U.S.S. Voyager. While Voyager is preparing to attack the Borg Cube, a smaller Borg Sphere appears through a transwarp conduit and hails them. Korok, a Klingon that has been assimilated into the Collective, has taken over the Sphere and offers to help them destroy the Cube. Chakotay accepts his offer and both ships begin attacking the Cube. Just as the Borg Cube explodes, Harry Kim manages to beam Janeway, Tuvok and Torres back to Voyager where they can be relieved of their Borg implants.
Seven, meanwhile, has gone back to Unimatrix Zero one last time to say goodbye to Axum. Axum and Seven are the only people left as Unimatrix Zero falls apart around them. Axum tells Seven that he is on a Borg Cube in a totally different part of the galaxy and though it seem like they will never see each other again, he will find her. They both leave Unimatrix Zero as it completely fritzes out of existence.
Seven of Nine watches as Rebi and Azan, two of the Borg children she had been taking care of since they were separated from the Collective, are reunited with their people, who agree to also give Mezoti a home. The only one of the Borg children staying aboard the U.S.S. Voyager with Seven is Icheb, the eldest of the four. After the children leave, Icheb notices that Seven is crying. Seven claims that her ocular implant is simply malfunctioning.
When Seven goes to see the Doctor, he confirms that there's a glitch in her cortical node, and he gets her to admit that she has been having headaches. Later, when Seven attempts to regenerate, she discovers she cannot interface with her alcove because her cortical node is malfunctioning. She stays up all night in the mess hall until Neelix arrives and offers to make her breakfast. Seven then falls to the floor convulsing, and Borg implants start bursting through her skin.
In sickbay, the Doctor realizes Seven's problem is more serious than he previously thought. Her cortical node, which regulates her vital functions, is destablizing, which means she will die unless it can be replaced. Captain Janeway gets an idea: She orders Ensign Kim to scan a nearby Borg debris field and transfer the coordinates to the Delta Flyer - she plans to salvage a replacement cortical node. Janeway, Lt. Paris and Tuvok depart for the debris field where they find several dead Borg drones and manage to remove the cortical node from one of them. Back on Voyager, Janeway and the Doctor practice the cortical node replacement operation several times in a holodeck simulation, failing miserably each time. They eventually decide that they cannot use a cortical node from a dead drone, but only from a living one.
Icheb also comes to realize that only the cortical node from a living Borg can save Seven, so he volunteers to have his own node removed and transplanted to her. Icheb devises a plan to have himself genetically altered to survive without his node, but the procedure is risky. When Icheb cannot get Janeway, Seven or the Doctor to listen to him, he programs the computer in his regeneration alcove to disengage his cortical node. Now dying, Icheb eventually convinces them to give his node to Seven and perform the genetic procedure on him. The operation is successful and both Seven and Icheb fully recover. Seven offers to help him study for the Starfleet Academy entrance exam, promising him a rigorous schedule. But then Icheb notices another tear in her eye... only this time it isn't a malfunction.
As Tom Paris and Harry Kim are taking the Delta Flyer for a test run, another small alien ship pulls alongside them. The alien pilot, Irina, challenges them to a race. As the two ships race through an asteroid field, Irina's ship begins filling up with nyocene gas. They beam Irina to their shuttle and bring her and her ship back to the U.S.S. Voyager. While making repairs, she explains to them that she is entering a race in a couple of days. This prompts Paris and Kim to convince Captain Janeway to let them enter the race too.
Meanwhile, B'Elanna Torres has been frantically trading favors with crewmates so she can borrow enough holodeck time for her and Paris, her boyfriend, to have an entire weekend to themselves. When Paris explains to her that he forgot about the getaway weekend and entered the race, she tells him that she does not mind. Later, she confesses to Neelix that she was very hurt that Paris forgot about something that took her so much time to set up. She tells Neelix that she thinks things might be ending between Paris and her.
When Janeway registers the Delta Flyer in the race, she learns from O'Zaal, the race coordinator, that the race is the first step towards peace for the four different cultures living in the area. Each of the different species has been at war to control the area for nearly a century. This race marks the first time the four of them have ever competed peacefully.
Seven of Nine tells Torres that she has embraced some of Paris' interests and it has made him easier to work with. Taking Seven's comment as good advice, Torres convinces Kim to let her fly with Paris as co-pilot of the Delta Flyer. Paris is bewildered when Torres shows up in Kim's place wearing a flight suit, but he welcomes her as long as she remembers that they're there to win. The two ride in fourth place for much of the race, but they eventually manage to take the lead. Just as they get into first place, O'Zaal calls a temporary stop, saying that one of the racers has had an accident.
Irina's control panel had malfunctioned and electrocuted her co-pilot, which was later determined to be intentional sabotage. O'Zaal decides to continue the race the next day. Kim offers to help Irina fix her ship and also fly as her new co-pilot, which she is hesitant about, but lets him do. Paris and Torres notice that Kim and Irina seem to be forming a relationship, which causes Torres to wonder how good of a match she and Paris are.
When the race continues the next day, Torres is distracted by her thoughts and Paris can sense something is wrong, but the Delta Flyer manages to maintain its lead. Irina and Kim have successfully fixed Irina's ship and begin to catch up with the others almost immediately, keeping track of the Delta Flyer the whole time on their computer.
When Paris finally asks Torres what is bothering her, they get into a heated discussion. Paris is determined to work things out, but Torres sounds like she is ready to give up. Paris stops the Delta Flyer and tells her they are not going to move again until they work it out.
Meanwhile on Irina's ship, her control panel malfunctions again, almost electrocuting Kim. Kim suspects that Irina sabotaged her own ship and has his suspicions confirmed when she points a phaser at him. He manages to wrestle the phaser away from her and finds she has disabled the com system, so he just stops the ship and holds her at gunpoint. When Irina seems strangely interested in the Delta Flyer's progress, Kims realizes that she has sabotaged that ship as well. She admits to him that the fuel converter on the Delta Flyer is rigged to explode at about the time it crosses the finish line, killing all of the spectators and officials in the area.
As Paris and Torres are beginning to work out their problems, Kim sends them a message about the fuel converter. They check their computer and discover that it will explode in a matter of minutes. They pilot the Delta Flyer to a nearby nebula and eject the warp core. The nebula contains the explosion and the Delta Flyer gets safely away.
After the race is over, Paris and Torres take the Delta Flyer out again on a more personal mission - the back of the ship now reads "Just Married".
A mysterious Bajoran man named Teero sits in a musty room with Bajoran tapestries and drawings of Maquis vessels, reciting a mysterious chant while staring at a monitor displaying crewmembers from the U.S.S. Voyager.
On board Voyager, Tom Paris surprises B'Elanna Torres by taking her to his new holoprogramła classic 20th century-style movie theater. In the theater, they discover that Crewman Tabor is sitting nearby completely unconscious. When the Doctor examines Tabor, he concludes that his injuries are the result of an attack, as evidenced by the microfractures on his cranium and contusions along his shoulder. Janeway then appoints Tuvok to investigate the case. Tuvok's initial belief is that a member of the crew is responsible.
Later, crewmen Yosa and Jor are working in engineering when Yosa reports that pressure is fluctuating. Jor then orders him to check the seals in the Jefferies Tube hatch. As Yosa crawls through the hatch, the lights suddenly go out. Then, a bright light shines in Yosa's face as someone approaches. Yosa, feeling threatened, crawls through another hatch but is unable to get the computer to seal the hatch shut. Again, the bright light shines on Yosa and he's knocked unconscious. Jor soon discovers Yosa and takes him to Sickbay. The Doctor examines Yosa and concludes that Yosa was attacked, having the same microfractures and contusions as Tabor. Janeway and Chakotay come to realize that all the victims are former Maquis.
Meanwhile, Paris and Kim are conducting an investigation in the holodeck Movie Theater, trying to capture a negative image that the intruder left behind. Their efforts show two humanoid figuresłone is Tabor and the other is not recognizable. Tuvok requests that they work on increasing the resolution of the images. Later, Tuvok tells Kim that for security reasons he read all crew mail in the last data stream from Starfleet, which includes a letter from Kim's cousin. Tuvok implies that Kim is a suspect, by pointing out that the letter mentions the Maquis killed Kim's friend years ago. As Kim defends his innocence, Tuvok becomes strangely perturbed. Later, Chakotay finds Torres unconscious in a cargo bay, and finds Tuvok heading towards him. To Chakotay's surprise, Tuvok grabs him by the throat and mind melds with him until he becomes unconscious. While Chakotay and Torres are treated in Sickbay, the other victims have woken up out of unconsciousness with no memory of what happened to them.
Tuvok continues the investigation sleeplessly, with no memory of attacking Chakotay. At Janeway's urging, he returns to his quarters to meditate. Suddenly, he gets flashbacks of victims in Sickbay, Yosa in the Jefferies Tube and Chakotay in the cargo bay. Then Tuvok enters the bathroom and sees Teero's reflection in the mirror. Frightened, Tuvok rushes to the holodeck where Janeway and Kim are investigating, and learns from the computer that he was in the Movie Theater during Tabor's attack and that the height and weight of the negative-image figure matches his own description. Tuvok then hears Teero's voice telling him to ignore his doubtsłand pulls a phaser. Tuvok soon gives up the weapon and admits to being the attacker, telling Janeway that he should be detained.
When Janeway visits Tuvok in the brig, he explains there is a voice trying to control his mind with Bajoran incantations. Tuvok also says that it was he who attacked Maquis crewmembers and performed mind melds on them, but without knowing why. Tuvok recounts that the attacks started after he received a letter from his son. Janeway, Chakotay, Seven and Paris then view the letter from Tuvok's son and discover that it contains a subliminal message, one of Teero chanting. Chakotay recognizes Teero and says that the Bajoran worked with the Maquis performing mind control experiments.
Janeway meets with Tuvok again in his cell to discuss Teero. Tuvok recalls meeting Teero seven years ago at a Bajoran temple. Then Tuvok gets a flashback of wearing Maquis attire and sitting in a surgical chair with devices attached to his head as Teero is performing a mind meld on him. Janeway urges Tuvok to tell her more, but Teero appears to Tuvok and tells him to complete his mission. Tuvok struggles to stay in control of his mind, but cannot. Instead, Tuvok sends Chakotay a command in the Bajoran language, and his behavior changes. Chakotay goes to Sickbay, fires his phaser at Paris and gives Torres the same Bajoran command. Together they gather the other former Maquis members who were also victims of Tuvok's attacks. They obey Chakotay's commands and fire at the Voyager crewmembers.
Meanwhile, the ship goes to red alert and Janeway tries to contact the Bridge, but there is no response. Chakotay finds her and announces that he is in charge. Chakotay tells Janeway that Teero helped them remember that they are Maquis members and that the rebellion on Voyager is not yet over. He releases Tuvok and detains Janeway in the brig. While the Maquis make plans to abandon the Starfleet crew on an M-class planet, Chakotay tests Tuvok's loyalty by commanding him to fire a phaser at Janeway. Tuvok fires the phaser, but nothing happens because the weapon is defective. Then, when Chakotay's back is turned to Tuvok, the Vulcan grabs Chakotay by the neck and performs a mind meld that brings Chakotay back to normal. After that, Chakotay hands control of the ship back to Janeway.
Eventually, the rest of the Voyager crewmembers return to normal, and Tuvok joins Janeway and the others at the movies.
Gar, a Dralian trader, enters an overcrowded, airborne hospital ship and looks for Chellick, the facility's administrator. Gar shows Chellick the Doctor's mobile emitter that he obtained from the U.S.S. Voyager. Gar fiddles with the controls on the device and the Doctor appears, but he immediately demands to be returned to his ship. The Allocator, the computer that prioritizes all patients on board the ship, announces that a generator has exploded and many patients are arriving. The Doctor witnesses the chaos surrounding him and decides his only option is to help. Chellick, Gar and Voje, another doctor, observe how the Doctor handles patients and are pleased with his work.
Back aboard Voyager, Kim is injured from a holodeck hockey match and visits the Doctor. When Paris and Kim talk to the Doctor, they notice something isn't quite right. Paris and Kim gather the others to examine the Doctor's mobile emitter; Torres announces it is a replicated fake. Neelix points out that Gar did spend a night in Sickbay and had ample access to the Doctor. Janeway then gives the order to search for Gar by scanning his ion trail.
Meanwhile, the Doctor is on Level Red of the hospital ship, scanning a young patient named Tebbis. The Doctor finds out that Tebbis has a deadly infection and has not received the proper treatment - cytoglobin - for it. Voje tells the Doctor that the patient's "T.C." level is not high enough to receive the necessary cytoglobin. Just as the Doctor asks what T.C. stands for, Chellick interrupts and says that he has acquired the Doctor's program from Gar. Chellick also says everyone on the ship must obey the Allocator's rules and that the Doctor must now provide his services on Level Blue. Then Voje explains that the patients on Level Blue receive the best treatment because their T.C. level is high. T.C., as the Doctor finds out, stands for "Treatment Coefficient," in which the Allocator assesses which patient has access to the best care depending on the importance of his or her profession, skills and accomplishments.
In the meantime, the Voyager crew is lead astray by Gar's trail. Then Tuvok recalls that Gar traded iridium with them and suggests they go to the location where Gar acquired the substance. They locate a mining operation on an asteroid and contact a resident. The man tells them that Gar sold them induction units, which came from a planetoid called Velos.
At the hospital ship, the Doctor finds the Allocator approving cytoglobin injections to all Level Blue patients. Another doctor named Dysek tells the Doctor that the injections increase the patients' life expectancy. The Doctor is concerned because he knows that Tebbis needs this medication to be cured. The Doctor sneaks to Level Red and tries to manipulate Tebbis' T.C. level by raising it higher, but the Allocator still denies medication. Then, the Doctor returns to Level Blue and takes a cytoglobin device from a nurse, whom he then dismisses. The Doctor returns to Tebbis with the smuggled cytoglobin injector and administers it to him. Later, the Doctor steals even more medication from Level Blue to treat the patients on Level Red.
Meanwhile, the Voyager crew enters the orbit of the planetoid Velos. They speak with an alien and find out that Gar is on Selek IV. The Voyager crew then locates Gar's ship and engages it in a tractor beam. They ask Gar where the Doctor is, but Gar refuses to tell them. After Gar is beamed aboard Voyager and questioned in the Brig, Neelix offers Gar a meal, which the prisoner quickly consumes. Suddenly, Gar experiences severe stomach pains. Neelix reveals that he poisoned Gar's meal and the Doctor is the only one authorized to administer the proper medication. Gar is then forced to tell them where the Doctor is.
Back on the hospital ship, the Doctor finds out that Tebbis was transferred to Level White - the morgue. The Doctor is angry and confronts Chellick, but Chellick reveals his knowledge of the Doctor's unauthorized injections and restricts the Doctor to Level Blue. Chellick also says that he interfaced the Doctor's holomatrix with the Allocator. Now, the Allocator will automatically monitor and delegate the Doctor's every move. Later, Chellick catches the Doctor on Level Red, but the Doctor injects Chellick with the same virus that inflicted Tebbis. The Allocator identifies Chellick as Tebbis and denies Chellick medication. The Doctor says that he will only help Chellick if Level Red is equipped with an adequate supply of medication. Chellick begs Dysek for help, but Dysek refuses his request, following the Allocator's rules - rules which Chellick established. The Doctor then proposes that Level Red patients, including Chellick, should be transferred to Level Blue to receive care. Chellick finally agrees.
The Voyager crew locates the hospital ship and retrieves the Doctor. Later, the Doctor aks Seven of Nine to check his ethical subroutines for any failures or changes, admitting that he had deliberately poisoned a man. Seven informs him that, unfortunately, he has "a clean bill of health."
After going without mail from home for over a month, the U.S.S. Voyager crew is looking forward to seeing the next datastream which is jammed in the ship's transceiver. Harry Kim and Seven of Nine determine that instead of letters, the datastream contains a hologram of Reginald Barclay, the Starfleet officer from the Pathfinder project on Earth who has taken a personal interest in getting Voyager home. Holo-Barclay tells Captain Janeway of the project's plan: Voyager will be passing through a sector of space occupied by a red giant star and at the same time, Federation scientists will target the magnetic field of another red giant in the Alpha Quadrant with a verteron beam to create a geodesic fold. As a result, space will be punctured at two points, creating a gateway between the quadrants. Janeway says the plan won't work because Voyager's shields are useless against geodesic radiation, but Holo-Barclay responds that he brought shield upgrades and medical technology to protect the crew.
The Doctor agrees to transfer his mobile emitter to Holo-Barclay so that the visitor can move freely about the ship while he makes preparations. In the briefing room, Holo-Barclay shows the crew where the geodesic fold will occur and passes out assignments to everyone.
In the Pathfinder research lab, the real Reginald Barclay investigates why the datastream transmission did not reach its target. Commander Pete Harkins, his supervisor, believes the hologram was lost because it was too complex and therefore it degraded, but Barclay insists something interfered. He comes to find that a spacecraft passed within 20 meters of the Midas Array just hours before Starfleet sent the first hologram, and conjectures that ship was either Borg or Romulan. Harkins refuses to listen, and orders Barclay to take a vacation.
Meanwhile in the Delta Quadrant, the Doctor tells Holo-Barclay that the medical inoculations are not strong enough to protect the crew from the geodesic fold's radiation, but Holo-Barclay assures the Doctor that in combination with the shield modifications, they will be enough. When the Doctor invites him to a game of golf, the hologram is evasive. Later, Torres and Kim prepare to transmit a "thank you note" back to the Alpha Quadrant, and Holo-Barclay asks to include his own "progress report." The datastream is transmitted to the Midas Array, but an alien device attached to the array diverts the transmission to a Ferengi ship near a red giant star. Three Ferengi on board huddle around a monitor to receive Holo-Barclay's report which includes information on Seven of Nine and her Borg nanoprobes. They intend to acquire those nanoprobes and sell them for a huge profit.
On Earth, Barclay catches up with his therapist and former crewmate Deanna Troi on vacation at the beach, and tells her about his distress. Troi recalls that Barclay was doing fine not long ago when he was dating a teacher named Leosa. Barclay reveals that Leosa expressed great interest in Pathfinder's plan, but then left him the same day that his hologram was lost. After prodding from Troi, Barclay admits that he suspects Leosa had something to do with the missing transmission.
On Voyager, Holo-Barclay proves to be the "life of the party" as he does impressions of the captain and Tuvok, to the delight of crewmembers. The Doctor calls Holo-Barclay to the holodeck and reminds him that they had an appointment to play golf. Holo-Barclay is strangely contemptuous toward his fellow hologram.
The real Barclay informs his superiors that Leosa is suspected of breaching Pathfinder security, and she is brought in for questioning by Admiral Paris. Leosa admits that she is not a teacher, but rather a dabo girl who works on a Ferengi casino ship. But she denies sharing her knowledge of the Pathfinder project with anyone. Troi knows she's lying, and coerces the truth from her, including the identity of the Ferengi ship involved in the theft. Scans find that ship near the red giant star, and Admiral Paris sends a starship to intercept it. Meanwhile, Leosa reveals to the broken-hearted Barclay that the Ferengi are after Seven of Nine's Borg nanoprobes, and that she would get a cut of the profit.
After his strange encounter with Holo-Barclay, Voyager's Doctor urges Janeway to run a diagnostic of the hologram since the crew is putting their lives in his hands. Janeway agrees, and the diagnostic shows Holo-Barclay is working perfectly.
While Admiral Paris and Commander Harkins are waiting for the U.S.S. Carolina to arrive at the red giant, Barclay tells Troi that he figured out what the Ferengi have done: They stole the first Barclay hologram that was sent a month ago, reprogrammed it to steal Seven's nanoprobes, and then smuggled it to Voyager in the next transmission. Meanwhile the Ferengi initiate a pulse in the red giant star to open a geodesic fold. This is seen back at Pathfinder, and the officers realize the Ferengi plan is to bring Voyager through the fold, which will kill the entire crew. On Voyager, Seven of Nine also realizes the crew will not survive the trip, so Holo-Barclay phases his holographic hand into Seven's cranial implant, causing her to fall unconscious. Since the Carolina won't arrive in time to stop the Ferengi, Barclay comes up with another plan.
The Ferengi ship receives a message from what they think is Holo-Barclay, who says that Captain Janeway found out about their plan, has developed a way to protect the ship as it comes through the fold, and will hunt down and kill the parties responsible. The three Ferengi believe him, and start closing the fold. They don't realize the message came from the real Barclay from a holodeck re-creation of Voyager at the Pathfinder lab.
Meanwhile, Holo-Barclay beams himself and Seven to an escape pod and heads toward the geodesic fold. Kim manages to beam them back aboard while the pod goes through the fold and rams into the Ferengi ship. The Ferengi are disappointed they didn't get their profit, and the Voyager crew are disappointed that yet another shortcut home failed. Meanwhile, Barclay is programming a new hologram with security precautions when Troi arrives to invite him to dinner, where she plans to set him up with a friend who's a real teacher.
The Doctor, Seven of Nine and Harry Kim are on a mission in the Delta Flyer to study preanimate biomatter from a comet. The ship jolts a few times and they realize they are under attack. The captain of the attacking vessel, Ranek, claims the Delta Flyer is transporting a "photonic insurgent" through Lokirrim space, which is forbidden. Kim explains that the "photonic," or hologram, is their Doctor. The patrol vessel grabs the Delta Flyer in a tractor beam and fires a disruption field that begins to decompile the Doctor's matrix. Kim then tells Seven that she must somehow hide the Doctor's program. The Lokirrim beam aboard with weapons demanding the photonic, but Seven announces that they "murdered" him. The boarding party inspects the vessel, and Ranek finds the Doctor's mobile emitter, which Seven claims is her "portable regeneration unit." Ranek confiscates the device regardless. He then orders the Delta Flyer to be secured in the Lokirrim docking bay, and locks Kim and Seven in a holding cell. It is here that Kim finds out that Seven downloaded the Doctor's program into her cybernetic implants, and the Doctor is now in control of her body. For the first time, the Doctor is able to have sensory experiences, including touch and smell.
On the U.S.S. Voyager, unaware of the Delta Flyer crew's predicament, Captain Janeway sets out to rendezvous with them in 48 hours. In the Doctor's absence, Tom Paris is examining Tuvok for a neurochemical imbalance, which turns out to be his Pon farr, the mating instinct that inflicts Vulcan adults every seven years. Paris promises to provide a special medication from the Doctor's database, and to keep his condition secret.
On board the Lokirrim patrol ship, the Doctor in Seven's body is enjoying the sensation of eating, even though their prison rations taste terrible, according to Kim. Ranek has Seven released and sent to the Delta Flyer for questioning. He asks her about the food replicator and whether it is used to create bio-weapons. Exasperated by his suspicious nature, Seven/Doctor replicates a slice of New York cheesecake to prove it's harmless, and experiences rapture upon tasting it. Before long, Seven/Doctor and Ranek have devoured plates of food and downed several glasses of wine. Despite being inebriated, the Doctor maintains the ruse of being Seven, and tells Ranek that she/he needs the "regeneration device" back. Ranek agrees to hand over the mobile emitter in exchange for medical services, then returns Seven/Doctor to the holding cell.
As Kim holds the mobile emitter, Seven/Doctor injects it with Borg tubules to restore the Doctor's matrix. The disoriented Seven then scolds the Doctor for abusing her body. The Doctor apologizes for his overindulgence, and thanks her for saving his life. The three then make a plan to get a message to Voyager, but it'll involve downloading the Doctor back into Seven's implants.
The patrol ship's tactical officer, Jaryn, takes Seven/Doctor to their medical bay and explains that the patients are suffering from synaptic failure caused by a viral weapon from their photonic enemies. As Seven/Doctor synthesizes a treatment, she/he gets to know Jaryn better and learns about the photonic servant who was part of her own family before the uprising. She/he suggests that Voyager's own "photonic," the Doctor, would have taken a liking to her.
On Voyager, the medication Paris applies to Tuvok isn't working to stabilize his condition. Paris suggests creating a replica of the Vulcan's wife in the holodeck in order to satisfy his longing, and Tuvok hesitantly agrees. While Tuvok participates in the holodeck simulation, the ship comes under attack by a Lokirrim vessel because of "photonic activity" aboard. Janeway agrees to shut down the holodecks and allow the Lokirrim ship to escort Voyager through their territory.
While Seven/Doctor is working with Jaryn in the patrol ship's medical bay, Ranek calls for Seven of Nine to meet him on the bridge. Ranek redirects the ship to a pulsar cluster called the "Window of Dreams," the most beautiful sight in the quadrant, and lets the pulsars' EM vibrations fill the bridge with natural music. Seven/Doctor doesn't realize he's trying to set a romantic mood, until Ranek can't help himself and plants a kiss on her/his lips. Seven/Doctor pushes him away and storms off. Seven/Doctor returns to the medical bay and tells Jaryn about Ranek's behavior, and learns that she has feelings for her captain. Since the Doctor has been developing feelings for Jaryn, he makes an impassioned plea for her to find someone more like him, when Seven/Doctor pulls a neck muscle. Jaryn starts massaging her/his neck, until she/he has certain feelings and pulls away nervously.
Seven/Doctor then gets called to the holding cell to treat Kim, who has been faking a seizure in order to get her/him back there. The Doctor separates himself from Seven into the mobile emitter, and Seven chastises him for kissing Ranek and for getting aroused by Jaryn. After the two argue about living life with or without indulgences, Kim presses them for what they've learned about the ship's com system. Seven now knows Ranek's command codes, and they need to get to the Delta Flyer to transmit them to Voyager. The Doctor conjures up a plan.
Seven/Doctor approaches Ranek and asks for a private meeting on the Delta Flyer, with an apology for her harsh reaction before, and a suggestion that they "start over." She/he offers him champagne, turns on music and starts dancing with him. When Ranek is called to the bridge, Seven/Doctor injects him with a hypospray and knocks him out.
Voyager gets a message from Seven that the away team is being held prisoner, and she provides their precise location and the command codes to disable the patrol ship's shields. Her personality and her comments cause Janeway and the others to realize that the Doctor is occupying her body, which means they're in more trouble than they thought. Janeway orders a phaser shot to the Lokirrim escort vessel, and Voyager makes a quick getaway.
At the patrol ship, Seven/Doctor has brought Ranek to the medical bay, telling Jaryn that he has an especially low tolerance for synthehol. Over Seven/Doctor's objection, Jaryn revives Ranek, who orders Seven back to detention, separate from the other prisoner, suspecting her of trying to aid the insurgents. They then receive word that an alien vessel is approaching, and Ranek takes Seven with him back to the bridge where he can keep an eye on her.
Janeway opens a channel to the patrol ship and demands the return of her people. When they refuse, Chakotay uses Ranek's command codes to disable their shields. Ranek ties the shields directly into their warp matrix, and announces that if Voyager fires, it'll trigger a core breach and their crewmates will die. Janeway sends a message directly to Seven's cortical node asking for her help to disable the patrol ship's shields. The Doctor materializes himself into the mobile emitter, and takes up a weapon while Seven works the shield controls. Ranek fires a weapon at the console Seven is working at, but she has already destabilized the shield grid. When he goes to the console to undo her work, it explodes, throwing Ranek across the bridge and seriously injuring him. Although the Lokirrim order him to stay back, the Doctor insists on treating Ranek, and he refuses to beam back to Voyager until he does, or else Ranek will die. Playing on Jaryn's feelings for Ranek, the Doctor gets her to let him operate.
Ranek is saved, and he and Jaryn both express their gratitude to the Doctor, even though their opinion toward "photonics" in general may not have changed. Back on Voyager, the Doctor is paid a visit in Sickbay by Seven, who brings delicacies and wine that she previously would have considered "indulgent." Since the Doctor can no longer share the experience of eating and drinking, Seven promises to describe the meal to him so he can enjoy it vicariously.
The U.S.S. Voyager sets down on a planet for a major maintenance overhaul while away teams in shuttles are sent in search of supplies. As B'Elanna Torres informs Captain Janeway that repairs will take days longer than originally expected, suddenly several consoles black out. Moments later the consoles flicker back on, and Icheb steps forward to explain the repair he made. Impressed, Janeway assigns Icheb to work with Torres, hoping he can help get the job done a little faster.
Harry Kim, Seven of Nine and Neelix are on the Delta Flyer searching for dilithium when they are caught in the crossfire between two alien ships. They receive a distress call from a Kraylor captain begging for help with casualties and claiming that his ship is on a humanitarian mission. Hesitant to get involved, Kim contacts the opposing ship, but the Annari commander there is very arrogant and charges weapons. Kim uses the Flyer's deflector to damage the Annari ship, forcing them to retreat. He and Neelix then beam over to the damaged Kraylor ship with medical kits and learn that the captain was killed along with all the ship's other officers. Kim sets out to repair the ship's engines and cloaking device, and impresses the Kraylor with his skills. When the ship is ready to fly again, Loken, the doctor in charge of the research team aboard, asks Kim to command the ship to their destination, since no one left alive among them is trained. Kim declines, but Loken insists that they can't afford to fail in their mission to deliver vaccines to their homeworld that will save thousands of lives. Since their flight plan will take them close to Voyager's location, Kim agrees to fly the ship that far.
When the cloaked Kraylor ship approaches the planet where Voyager is grounded, they discover three Annari warships in orbit. It turns out the Annari are attempting to befriend the Voyager crew and become trading partners. Once the Annari leave the planet, Kim brings Loken to Voyager, where he appeals to Captain Janeway for help getting home. In private, Janeway tells Kim that he has put her in a difficult position, but Kim presses the case on behalf of the Kraylor, and offers to take charge of the mission himself. He notes that after seven years on Voyager he's still an ensign, and wants a chance to prove himself as a commander. Janeway agrees, but orders him to take Seven along.
After getting a lesson in decisiveness from Neelix, Kim enters the bridge of the Kraylor ship with authority and lays in a course. He renames the ship "Nightingale" after the famous wartime nurse from his homeworld. He then prepares the ship for departure and gives the command to engage. During the flight, Seven informs Kim that she asked the acting helmsman, Terek, to make a course correction. Over Seven's objection, Kim goes to check up on the crewman and ends up doing the job himself.
Meanwhile on Voyager, Icheb has been working with Torres, who invited him to go rock climbing with her on the holodeck. After he gets advice from the Doctor on how to tell if someone has romantic feelings for another, Icheb thinks he's getting "signals" from Torres while working very closely with her in a Jefferies tube, and even scans her for the physiological responses the Doctor described.
On the Nightingale, an alarm sounds and the cloak destabilizes. Kim orders all stop and works in Engineering with Seven and crewman Dayla, making the repairs himself and rejecting the suggestions of the others. Seven criticizes Kim's overly hands-on and dismissive approach to commanding the crew, but Kim proceeds to order the ship to resume course. The cloak soon fails again, and six Annari vessels swoop in and fire upon them. While Seven tries to get the cloak back on-line, an explosion in Engineering knocks her unconscious. Kim tries to leave the bridge, but the crew insists he stay, so he lets Dayla go down to Engineering while he gives her instructions over the com. As he's doing that Loken suddenly interrupts and gives Dayla different orders, which succeeds in re-engaging the cloak. Kim eyes Loken suspiciously as he orders the ship to escape at full impulse.
Later, Loken reports that Dayla is dead while Kim tries to treat the still-unconscious Seven. Kim tests Loken by asking his advice as a doctor, having realized that he knows a lot more about cloaking systems than he does biology, as did Dayla. He presses Loken for the truth, and the Kraylor admits that he and his colleagues have not been developing vaccines, but rather cloaking devices for his people's fleet. The so-called medical transport is actually a prototype ship, and the Annari don't want it to reach the Kraylor homeworld. He reveals that his planet has been under an Annari blockade for three years which has been choking off supplies of food and medicine, therefore their mission is still a humanitarian one. Nevertheless, the angered Kim orders the ship to reverse course back to Voyager. But the crew refuses to obey, and Kim realizes he's lost command.
Back on Voyager, Icheb gets flustered when Paris jokes that he's been spending a lot of time with his wife lately. Icheb approaches Torres and tells her outright that they should not be romantically involved. Torres is dismayed, but she plays along and agrees that they should stop "seeing each other."
When Seven of Nine comes to, Kim tells her about the situation and that they should take an escape pod back to Voyager. Seven asks if he's abandoning ship because the mission isn't what he expected, or that being a captain isn't what he expected. In spite of his remorse over Dayla's death, she exhorts him to fulfill his commitment to get the Kraylor home, because they won't survive without him.
As the Nightingale approaches the Kraylor homeworld, the crew sees Annari ships in orbit emitting pulses of energy designed to illuminate cloaked ships. Unsure how they will get through that barrage, Kim comes back to the bridge and promises to find a way.
Voyager receives a hail from the Annari captain who befriended them earlier, ordering Janeway to leave Annari space immediately because they've discovered her people are supporting their enemy. The warp engines are not repaired yet, but Janeway has no choice but to let Voyager be escorted away at impulse speed.
Meanwhile, the Nightingale is detected and gets fired upon by Annari ships. Kim opens a channel to the lead Annari vessel and offers to discuss terms for surrender. He tells his crew to trust him as he proposes to the Annari that they be allowed to evacuate to the surface in exchange for turning over the ship with its cloaking technology, otherwise he'll self-destruct the ship. The Annari commander agrees, but Kim has a plan. Kim, Seven and Terek stay aboard while Loken and the others leave in escape pods. Kim tells Seven to get the exact polarity of the Annari's tractor beam in order to use their own weapons against them. At just the right moment, the Nightingale reverses shield polarity and snaps free, heading for the Kraylor defense perimeter. They outrun the Annari and get through the planet's shield grid, and the Annari break off pursuit. Kim orders Terek to take them to the surface, completing his mission. Back on Voyager, Kim notes in his log that although the mission was a success, he doesn't feel entirely good about it, and he confesses to Neelix that he's not a captain...not yet, anyway.
Two Hirogen move through a jungle hunting prey. Suddenly phaser shots are fired at them from a small lake. Four armed Starfleet crewmen rise out of the water and continue firing, destroying their predators with vengeance.
The U.S.S. Voyager receives a distress call on a Hirogen frequency and approaches a mysterious vessel. An away team beams over and finds themselves in a jungle, and upon surveying the area, they discover the bodies of Hirogen killed with Starfleet-issue phasers. They are also surprised to find a Klingon bat'leth stained with Hirogen blood. The team detects a lifesign that appears wounded, and upon approaching a cave, they are fired upon. A panicky Hirogen civilian, Donik, warns the visitors away and continues firing his weapon. Tuvok sneaks up behind Donik and renders him unconscious with a nerve pinch. The Hirogen has lost a lot of blood, so Paris beams him to Voyager's Sickbay. Meanwhile the away team finds a holodeck interface of Starfleet design, and they realize the jungle environment is simulated, and wonder why their tricorders didn't detect that fact. Seven shuts down the holodeck emitters, and they find themselves in a hologrid filled with dead Hirogen.
Back on Voyager, Chakotay tells Captain Janeway the holo-technology she gave the Hirogen three years ago so they could hunt holographic prey was apparently modified to be more dangerous. The Captain is astonished that the Hirogen obviously "missed the point" and got themselves killed. She approaches the terrified Donik in Sickbay, and after convincing him she is not a Hologram, learns that the vessel he was on is a training facility where young Hirogen learn to hunt. He is a technician who was maintaining the system when the Holograms malfunctioned, took control and deactivated the safety protocols.
Just then, a Hirogen ship intercepts Voyager and starts firing. The Alpha-Hirogen in command demands that Voyager leave immediately, but Janeway informs him that she has the one survivor from the facility on board. The Alpha- and Beta-Hirogen beam over and confront Donik, accusing him of being a coward for hiding from the Holograms while hunters fought and died. Donik reveals that the Holograms transferred their programs to a vessel equipped with holo-emitters, and are on the loose.
The Hirogen team up with Voyager's crew to locate the renegade Holograms. Once they detect their ship, the Hirogen prepare for the "hunt" and Janeway insists on joining them, feeling partly to blame for the situation. The Hirogen vessel moves in for the kill over Janeway's objections, and after it's too late they realize the ship they see is a decoy -- it's really a bomb, which explodes and seriously damages the Hirogen vessel. While Voyager beams over the survivors, the actual ship occupied by the Holograms drops out of warp and starts firing. The Holograms then tap into the holo-emitters in Sickbay and transfer the Doctor's program to their own ship, then immediately go to warp, masking their signature so they can't be followed.
The Doctor materializes on the Holograms' ship and finds himself surrounded by simulations of various Alpha Quadrant species. A Bajoran hologram named Iden welcomes the Doctor aboard. He demands to be returned to Voyager, but Iden says they have "wounded." The Doctor says he's not an engineer and has limited experience in repairing holograms, but Iden insists that he try.
At Voyager, Janeway learns that the Holograms are very sophisticated and have the ability to learn and adapt, so they will be hard to disable. Donik confesses that he modified the Holograms under his Alpha's orders to make them formidable prey. Janeway approaches the Beta-Hirogen, who is in charge now, and lets him know she found out about the modifications, and points out that they created prey with skills that surpass their own. The Beta-Hirogen says he will resume the hunt, but Janeway insists they must find a way to take the Holograms offline from a safe distance, and do it with the Hirogen's help or else she'll leave them on the nearest habitable planet. The Beta-Hirogen has no choice but to agree.
At the Hologram ship, the Doctor finds a way to perform a "subroutine transplant" in order to repair a Klingon hologram, and succeeds with the help of Kejal, a highly intelligent Cardassian hologram. The Doctor is shocked to find Holograms bleeding and experiencing pain, and Kejal explains that the Hirogen programmed them to suffer when they are killed. Once he's done treating the injured, the Doctor finds Iden praying at a Bajoran altar, and wonders how someone who's programmed with spiritual beliefs could perform such a massacre. Iden explains that his Alpha-Hirogen would hunt him and kill him over and over, causing him to live in fear and pain. With the ability to adapt, he became cunning enough to escape, and joined other photonic beings who were being oppressed by various races in the sector and who had chosen to fight back. The training facility they just left was actually the third one where Iden "liberated" the holograms. Iden tells the Doctor his life will never be his own as long as he is controlled by organics, and asks him to stay and make a new life with his own kind. The Doctor refuses.
Soon after, the Doctor finds himself running through a jungle, being hunted by Hirogen. The confused and terrified Doctor gets wounded and starts bleeding, then he's stabbed to death. The Doctor wakes up in shock on the Hologram ship. Iden explains that they transferred memory files from one of their Holograms into his program so he can come to understand what they've been through. Enraged, the Doctor accuses them of being thugs looking for a fight. But Iden says what they're looking for is a home where the Hirogen can't hurt them anymore. His sympathy growing, the Doctor asks to hear more about this "home." Iden and Kejal show the Doctor a photonic field generator, which they plan to deploy on a planet's surface to create a holographic environment they can live in. The Doctor suggests that the Voyager crew could help, especially Lt. Torres, who's an expert on holo-emitters. Iden does not trust organics, but is interested in knowing more about Torres.
At Voyager, Donik discusses strategy with Janeway, Seven of Nine and Torres on how to shut down the Holograms, and Torres embarks on a plan to reconfigure the ship's deflector to emit an anti-photon pulse. Soon afterward, the Hologram ship intercepts Voyager and hails them. The Doctor appears on the viewscreen and says the Holograms have come to make peace. He comes back aboard and tells Janeway that the Holograms want to create a new life for themselves and need Voyager's assistance. Janeway is hesitant to share technology again, because that's how the problem got started. The Doctor gets frustrated and tells her the Holograms are a new species, one that she helped create, and she can't turn her back on them. Janeway and the Doctor argue contentiously over "holographic rights" when they get word that a fight has broken out in the Mess Hall where the Hirogen are being confined.
The Hirogen are creating chaos so that the Beta-Hirogen can get to a control panel and access the com system. Tuvok arrives and stops him, but he has already summoned two Hirogen vessels. With less than an hour to intercept, Janeway orders Torres and Donik to prepare the deflector to take the Holograms off-line so there will be no more bloodshed. The Doctor objects to having them deactivated, but Janeway proceeds and contacts Iden, telling him to prepare his people to be transferred to Voyager's database. Iden doesn't trust that Janeway, an organic, will ever reactivate them. He ends the transmission, fires on Voyager and begins moving away. The Doctor pleads for Janeway's reconsideration, but she orders him to go help Paris treat the wounded in the Mess Hall. The Doctor leaves the Bridge, but in a crisis of conscience, goes to Sickbay instead. He contacts Iden and transmits data on the pulse about to be used to deactivate the Holograms, along with Voyager's shield frequencies so they can beam him off the ship. The Doctor transports over while Voyager and the Hologram ship exchange fire. Iden had given his word he wouldn't use the shield frequencies to attack Voyager, and he keeps that promise, but when Voyager emits the deflector pulse, he sends a feedback surge through the beam that overloads the ship's deflector and causes an imminent warp core breach. As Torres puts up a forcefield to reinforce the core, an energy tendril knocks her out. Iden beams Torres over to his ship, then escapes to warp as Voyager is left adrift.
The renegade Holograms have disabled Voyager and escaped to warp, but not before abducting Lt. Torres in hopes of benefiting from her expertise with holo-technology. The Doctor, who voluntarily joined the renegades, is furious with the group's leader, Iden, but Iden promises to let Torres go once she has a chance to decide for herself whether to help the Holograms. Meanwhile, the Voyager crew struggles to repair the ship in Torres' absence, and Janeway learns that the Doctor betrayed and abandoned the ship, and wonders if his matrix may have been altered by the other Holograms. When Torres wakes up on the Hologram ship, she intends to leave immediately, and rebukes the Doctor for switching allegiances. The Doctor points out she did the same thing as a Maquis, and tries to convince her that by providing her technical expertise, she can help stop the violence. He takes her to meet Iden, and she agrees to look at the photonic field generator, but makes no promises.
On Voyager, the crew has no luck locating the Holograms. Donik thinks he can modify the ship's sensors to detect them, and asks to stay aboard rather than go back with the other Hirogen. Two much larger Hirogen vessels arrive and retrieve all their people except for Donik, and the new Alpha-Hirogen threatens to turn the Voyager crew into prey if they interfere with their hunt. The Hirogen vessels go to warp, and Janeway decides to follow using a plan by Donik to hide Voyager in the ion wake of one of the Hirogen vessels a "blind spot."
Torres looks at the photonic field generator with Kejal, suspicious of the Holograms' motivations. When she comes to realize she's prejudged these beings, Torres proceeds to help enhance their technology. Meanwhile, Iden approaches the Doctor, who is having doubts about being with the Holograms. Iden shows him their destination: a Class-Y planet he calls "Ha'Dara," which is Bajoran for "Home of Light." He plans to install the generators on that planet because its environment is toxic to organic life, so they'll be left alone there. Just then, the Holograms realize that two Hirogen vessels have detected them, so they proceed to hide in a nebula. The Hirogen ships also fly into the nebula, unaware that Voyager is trailing one of them from within its ion wake.
The Holograms try to evade the Hirogen while Torres works a little faster to get the field generator on line. She successfully tests the generator by running Kejal through it, and lets the hologram know that as the closest thing they have to an engineer, she's the most important member of her crew. Meanwhile, the Doctor tells Iden that in their new society on Ha'Dara, he hopes to expose the others to music and art from various worlds. Iden responds that the Holograms will develop a culture of their own without emulating organics. In fact, he plans to establish a new religion with himself being worshipped as the "Man of Light" who delivered his people to freedom. The Doctor's doubts grow stronger.
A Nuu'bari mining ship is detected, and Iden orders an intercept course, planning to liberate the holograms on board. The Doctor expresses his concerns to Torres, revealing that Iden is showing signs of megalomania. Meanwhile, the Hirogen detect the Hologram ship on the other side of the nebula and move to intercept, with Voyager surreptitiously tagging along. On the Hologram ship, Iden contacts the Nuu'bari miners and tries to coerce them to turn over their holograms. They refuse, so Iden fires upon them and has Kejal steal the hologram programs. The Nuu'bari threaten to retaliate, so Iden targets torpedoes upon their warp core and destroys them, to the Doctor's and Torres' horror. He then sets a course for Ha'Dara as Torres accuses him of murder. He has her confined and then asks Kejal to bring their new "friends" on-line. Because their programs are incompatible with their emitters, she needs Torres' help, who agrees because she thinks she can get through to Kejal. As they work, Torres lets Kejal know that Iden doesn't have to be the one to make all the decisions, and she has the power to deactivate him. Finally the Nuu'bari holograms come on-line, but they are incapable of any interactions - they are only programmed with very rudimentary subroutines. Torres points out that Iden killed two living beings to "liberate" mindless machines, but Iden fervently declares that they are "children of light" and he will deliver them to freedom. Just then the bridge announces they are approaching Ha'Dara. Iden orders the generator to be deployed immediately, and refuses the Doctor's request to release Torres.
The Hirogen follow the Holograms to the planet, and when they drop out of warp, Voyager immediately fires weapons and disables both hunting vessels. Voyager then turns on the Hologram ship. Iden has the Hirogen hunters transported to the planet's surface so that the Holograms can hunt them in retaliation. The Doctor objects to his actions, so Iden deactivates his program, but not before assuring him that he'll be remembered in their prayers. He takes the Doctor's mobile emitter and transfers his own program to it, and orders the field generator transported to the surface. He rallies the other Holograms, declaring that this time, the hunt is theirs.
On the surface, the unarmed Hirogen have trouble breathing. The Holograms materialize around them and begin pursuing them with weapons. Meanwhile on the ship, Torres convinces Kejal to stop the massacre, but their transporters and communication system were damaged by Voyager. Torres tells Kejal to shut down the Holograms, which she does, and the Holograms on the surface dematerialize before they can kill more Hirogen. However, Iden is using the mobile emitter, so she can't deactivate him. Torres suggests sending the Doctor to the surface through the generator.
The Doctor materializes on the planet with a Hirogen hunting rifle, and he begins pursuit. Just as Iden is about to kill the Beta-Hirogen, the Doctor catches up with him and demands he lower his weapon. Iden refuses, so the Doctor fires and obliterates his fellow Hologram.
The surviving Hirogen are rescued by Voyager, and after recovering, the Beta-Hirogen intends to reclaim the Hologram vessel along with everything in its database. But Neelix convinces him that the stories that are told about this hunt will reflect more favorably upon him if the Hologram ship is thought to have been destroyed. The Hirogen agrees, and leaves Voyager empty-handed. Janeway transports to the Hologram vessel and learns from Torres that Iden is unrecoverable, but the other Holograms are intact in the database. Janeway offers Kejal refuge on Voyager, but she insists that this ship is her home, and Donik volunteers to stay with her and reprogram the Holograms to undo some of the damage he caused. Torres vouches for them, and Janeway urges them to always consider the consequences of their actions, which she's saying just as much to herself as the others. Back on board Voyager, the Doctor offers to let Janeway take his mobile emitter away and revoke his freedom, but she won't punish him for becoming as fallible as those who are made of flesh and blood.
While Icheb tutors Naomi in genetics and Chakotay joins Janeway for dinner, Voyager gets rocked by the gravimetric force of a spatial rift. Chakotay heads to Engineering when the ship's warp core begins to destabilize, and as he tries to maintain containment, an energy blast strikes him and knocks him out. Chakotay and the ship both shimmer in a strange patchwork effect. Torres checks Chakotay and sees that half his face is aged and the other half is youthful, and has him beamed to Sickbay. Chakotay wakes up in Sickbay and learns that his body was in a state of temporal flux, but the Doctor created a chronoton-infused serum that brought him back to normal. Chakotay asks the Doctor to come with him to check for other injured crewmen, but the hologram says he can't leave Sickbay. Chakotay asks about his mobile emitter, but the Doctor doesn't know what he's talking about. Chakotay can tell something is wrong and leaves.
Chakotay ascends in the turbolift and a distortion wave passes through it, causing the medkit he was holding to disappear. Chakotay enters the Bridge and asks Kim what's going on. Kim doesn't recognize him, but Janeway does, and orders guards to take him into custody, accusing him of sabotage on behalf of the Maquis. Chakotay realizes he's somehow been thrown seven years into Voyager's past. As he rides the turbolift with the guards, another distortion wave causes the guards to disappear. Chakotay then proceeds to Engineering and he finds it occupied by Kazon warriors and his old lover-turned-nemesis Seska. After they knock him out and revive him, Chakotay realizes he's in a time period five years ago when Seska (restored to Cardassian form) and the Kazon took control of Voyager. He tries to tell Seska what's going on, but she won't listen, so he has to bluff his way out of captivity. He manages to climb to an upper level in Engineering and passes through a distortion, and disappears from Seska's point of view.
Chakotay returns to Sickbay and tells the Doctor that the ship has somehow been fractured into different time periods, and that the serum injections seem to allow him to pass through the barriers between them. Chakotay asks the Doctor to give him the same serum in a hyospray that can also pass through the temporal barriers, so that he can put the ship "back together" again. He goes back to the bridge and approaches the Janeway of seven years past, telling her personal things about herself that he couldn't know. She starts to listen to his story and his plan, but still suspects him of nefarious intent, so he forces the serum injection upon her and takes her through a time barrier. Starting to gain her trust, Chakotay takes Janeway to the Astrometrics Lab which has temporal sensors that can help them map the time distortions. On the way they encounter injured crewmen in a corridor, in a time during one of Voyager's many predicaments, and Janeway gets increasingly perplexed. In Astrometrics, Chakotay and Janeway find a grown-up Icheb and Naomi 17 years into the future. They reveal that Chakotay and Janeway both died in the accident that shattered the space-time continuum aboard the ship. Janeway theorizes that if they can get to a section of the ship that still exists in the time period where the chronokinetic surge occurred, maybe they can counteract it. They could use the help of Seven-a name Janeway doesn't recognize-so Chakotay suggests finding her in another time frame.
Chakotay takes Janeway to the Cargo Bay where the Borg have entrenched themselves during Voyager's temporary alliance with them. Seven of Nine, who is still fully a drone, says a chronoton field generated by the warp core and projected throughout the vessel would force it back into temporal sync, and Chakotay would have a few seconds to counteract the energy surge that caused the problem. Janeway gets the idea of injecting the ship's bio-neural circuitry with the Doctor's serum in order to transmit the chronoton field. Chakotay and Janeway get the Doctor to replicate more serum, at which time the Doctor accidentally reveals to Janeway that the crew will get stranded in the Delta Quadrant.
Janeway and Chakotay begin going throughout the ship to inject the neural gel packs with the serum. In a corridor, they are chased by a macrovirus from another incident in Voyager's history in the Delta Quadrant, leaving Janeway further bewildered. They then enter a monochromatic environment in the ship's holodeck, which is Paris' "Captain Proton" program. Just when they find the panel they need, Doctor Chaotica and his henchmen appear and restrain them. Unable to deactivate the program, Chakotay tells Janeway to play along in the role of Arachnia, Queen of the Spider People. Rolling her eyes the whole time, she convinces Chaotica that she is loyal to him, and gets him to inject the gel pack himself.
In a transporter room, Janeway and Chakotay encounter several Maquis members, including Torres before she joined the Voyager crew. Torres accuses Chakotay of collaborating with the enemy, but he gains her trust and injects the gel pack. They next go to the Mess Hall, where Paris has set up triage for several crewmen injured in the original incident. Janeway finds her friend Tuvok, who is afflicted with radiation burns and dies while holding her hand. After leaving that location, Janeway tells Chakotay that she can't let all this happen again, and wants to put Voyager into temporal sync with her own time frame. She intends to change the future, the Temporal Prime Directive be damned. Chakotay sets her straight by pointing out that she's seen bits and pieces of the future, but not the whole picture. Despite the problems that Voyager has encountered, much has been gained through the crew's experiences, such as Seven of Nine recovering her humanity and Paris and Torres getting married, and the Maquis and Starfleet crews coming together under a captain who would never stop believing they would get home.
Their final stop is Engineering, where Chakotay has to deal with Seska. His story is so preposterous that she believes him, so she lets him inject the gel pack, but realizing that his presence means the Starfleet crew will regain control of Voyager, she demands that he modify the plan by bringing the ship into temporal sync with her time frame. He refuses, so she threatens to kill him. However, Janeway is waiting in the upper level, along with Paris and Kim who have been injected with the serum. They storm the Kazon contingent, and on that cue, the adult Icheb and Naomi rush in from one side of the room while Torres and another Maquis come in from the other side to surprise the Kazon and wrestle away their weapons. But Seska manages to grab Janeway and hold her hostage with a phaser. She demands inoculation for herself and her people, or Janeway will die, but at that moment Seven of Nine appears through a temporal barrier. Seska fires at the drone, but Seven's Borg forcefield repels the phaser shot and she overtakes the Cardassian, saving a thankful Janeway.
Janeway has everyone return to their section of the ship, pointing out that once the timeline is restored that will have no memory of what happened. Chakotay works the warp core as Janeway returns to the bridge. The chronoton pulse is initiated, and the ship is restored to the original time frame but a few seconds earlier. Chakotay immediately orders Torres to reroute main power to the ship's deflector so it can serve as a "lightning rod." The energy discharge from the spatial rift hits the deflector dish and burns it out, but the warp core is unaffected and the ship is saved. Chakotay refuses to tell the present-day Janeway why he made that order, invoking the Temporal Prime Directive, but that doesn't keep them from finishing their dinner together.
B'Elanna Torres starts the morning in an uncommonly good mood, but then in Engineering her mood changes and she scolds Icheb for being there without her permission. Suddenly she gets dizzy and drops to the floor. Seven of Nine goes to help as Icheb scans her with a tricorder. Icheb says he detects a lifesign inside Torres, perhaps a parasite. But Seven contacts the Doctor and tells him Torres may be pregnant. In Sickbay the Doctor confirms to Torres and her husband Tom Paris that they are indeed having a baby, and the reason Torres fainted could be that Klingon and human metabolism sometimes clash. The fetus is healthy, but the Doctor warns Torres that she can expect to experience some behavioral volatility.
Despite Tom and B'Elanna's wish to keep the news to themselves for awhile, the rest of the crew quickly finds out about Torres' pregnancy, and both Neelix and Chakotay vie to be the child's godfather. Captain Janeway offers Torres time off, but Torres insists that she can handle her duties. Meanwhile an increasingly anxious Paris faces the prospect of being of father, and even solicits advice from Tuvok. Later Paris has a candlelight dinner set out when Torres returns to their quarters, but she's upset about the Captain practically relieving her of duty and annoyed by crewmembers' unsolicited advice. She gets further upset when Tom makes a comment about her being a Klingon mother. B'Elanna catches herself in "behavioral volatility" and calms down, but then the Doctor summons them to Sickbay.
Tom and B'Elanna learn their child's spine will be deviated, but that a genetic modification will correct it. The Doctor also accidentally reveals that it's a girl. At Tom's request, the Doctor projects an holographic image of the baby. Tom thinks she's beautiful, but B'Elanna wonders why the girl has forehead ridges when she's only one-quarter Klingon. The Doctor says Klingon traits remain dominant for several generations. B'Elanna has a flashback to a time when she was a young girl on a campout with her human father, and recalls that he told her how much she was like her Klingon mother. Later, Paris and Torres turn in for the night, and Torres continues to recall the campout experience from when she was 12 years old. Young B'Elanna didn't want to go hiking with her human cousins because she thought they didn't like her.
The next morning Torres reports to Sickbay to undergo the Doctor's recommended genetic treatment. While lying on the bio-bed she has another flashback from the campout: one of her cousins, an 11-year-old boy, put a worm in her food and teased her about being Klingon, causing young B'Elanna to storm off. After the Doctor completes the treatment successfully, Torres goes to a holodeck and projects a computer-generated image of her daughter when she will be 12 years old. Seeing her forehead ridges, Torres examines the child's genetic makeup, and deletes certain gene sequences in the computer display. Asking the computer to extrapolate the genetic changes to the projection, she eventually causes the girl to look completely human. Torres saves the changes and restricts access to the file for herself.
Torres returns to Sickbay and tries to convince the Doctor to make further genetic changes in her baby, claiming it will prevent potential health problems. The Doctor is against the idea and suggests that she talk this over with Paris. When she does, Paris is totally against the idea. He comes to realize the issue is not about the child's health, but the fact that the child is part Klingon. He tries to assure her that their daughter will not be treated like an outcast. But they fail to come to an agreement, and turn to Captain Janeway. Torres argues that she wants to make physiological changes for her child's best interest, just as Janeway did for Seven of Nine. Janeway points out their problem is not ethical, but marital, and she would not overrule the Doctor. Torres is not happy that Paris has gotten his way, and before he knows it he's at Harry Kim's doorstep needing a place to sleep.
Torres sits in bed alone, recalling more of the campout experience. Young B'Elanna finally returned to the campsite after having run off, and told her father, John Torres, that she wished she wasn't Klingon because everyone made fun of her and her schoolmates hated her. Despite her father's assurances that the other kids didn't hate her, young B'Elanna chose to sit alone and read rather than join the rest of her family around the campfire. In the present moment, Torres re-experiences the isolation she felt back then.
While working in Engineering the next day, Torres recalls when she overheard her father talking to Uncle Carl about how moody and argumentative young B'Elanna had become, just like her mother. John reminded his brother about their parents' reservations about him marrying a Klingon, and noted that now, ironically, he was living with two of them. Later Torres meets up with Paris in the corridor, and they reconcile. They are then summoned to Sickbay.
The Doctor tells Torres and Paris that he reviewed the data and has concluded the genetic alterations she wanted are necessary because the "clash" between Klingon and human metabolism is more extensive than he realized. The child risks complete metabolic failure, and to prevent it he must eliminate most of her Klingon genetic material. The Doctor schedules a procedure for the next morning. Meanwhile a disturbed Paris takes the Doctor's findings and runs it by Icheb, who spots a computational error. Seven runs a diagnostic on the Doctor and discovers that his program has been tampered with. Paris tries to contact Torres, but she doesn't respond. The computer reveals she's in Sickbay. Torres has already arranged to undergo the procedure to alter the baby.
Torres has blocked communications to Sickbay and access to the Doctor's program, so Paris, realizing that Torres manipulated the Doctor to "change his mind," summons Tuvok to meet him at Sickbay. They have to manually open the door, and then encounter a forcefield. Paris orders the Doctor to stop the procedure, but Torres tells the Doctor to ignore him. Eventually the forcefield is cut off and Tuvok informs the Doctor he's been altered, so he agrees to deactivate himself. Tuvok leaves Paris and Torres alone. The couple argue over Torres' actions, and in the heat of the moment Torres reveals her issue is with her father. She tells Tom about how she and her father grew apart, and during the campout when she was 12, she blurted out to her father that if he can't stand living with two Klingons, why doesn't he just leave. And several days later, he did. Tom realizes she has blamed herself all this time for her father leaving, and she fears the same thing will happen again. He assures B'Elanna he will never leave her, and he hopes to have even more Klingon children and that every one of them is just like her. Later, Torres reverses the alterations to the Doctor, and while apologizing to him she feels the baby kick. Now she's happy about having a feisty Klingon in her womb. She asks the Doctor to be the child's godfather, and he elatedly accepts.
Responding to a distress call, the U.S.S. Voyager approaches a damaged alien vessel and transports two injured passengers to Sickbay and nine others to a Cargo Bay. In the Cargo Bay, three of the rescued aliens are Nygean guards holding the others prisoner, and they are concerned that their weapons didn't beam over because the other men are dangerous criminals. In Sickbay, another prisoner named Iko takes Seven of Nine hostage and demands a ship and some food. Tuvok arrives with the Nygean warden, Yediq, who says he won't negotiate with criminals. Iko is distracted and Seven breaks free from his grasp. He then grabs the Doctor, but Tuvok fires his phaser through the holographic Doctor and strikes Iko to the floor.
Later, Yediq thanks Captain Janeway for saving them, and he tells her, Chakotay and Tuvok that the prisoners are being transported back to the Nygean homeworld for execution, because they have all been convicted of murder. The officers are uncomfortable that their ship will help deliver eight men to their deaths, but they are bound by the Prime Directive, so Janeway agrees to keep the prisoners detained for several days until a Nygean ship can make a rendezvous. Tuvok outfits the Cargo Bay with prison cells secured by forcefields and tritanium bulkheads, and the prisoners are held there, including Iko, who is beamed over from Sickbay after threatening to kill the entire crew unless he is released.
While Tuvok lays down the ground rules to Yediq, Neelix arrives with a dinner cart. Yediq tells him to take it back because the prisoners don't deserve such an elaborate meal, but Neelix and Tuvok cite Federation protocols regarding the treatment of prisoners, and Yediq relents. Meanwhile, the Doctor expresses to Seven how troubled he is by the captain's arrangements with the Nygeans, because he believes their death penalty is barbaric.
In the Cargo Bay, a prisoner named Joleg provokes Iko into causing a disturbance, and when Yediq checks on him, Iko threatens the warden's children. The Nygean guards enter Iko's cell and beat him severely, but then Voyager security officers jump in and stop the violence. Afterwards Janeway is infuriated with Yediq and bans him and his men from the Cargo Bay, putting Tuvok in charge of the prisoners. The Doctor treats Iko in Sickbay, and asks Seven to provide nanoprobes so he can program them to repair the neurological damage done to the prisoner's brain.
Meanwhile Neelix delivers food again to the prisoners, and Joleg tells him that he ended up among the condemned because he was found in the vicinity of a murder, and was arrested and convicted simply because he is Benkaran - a species "known" by the Nygeans to always be criminal. Later, Neelix contacts the Nygean government under the pretense of a "cultural exchange" and acquires data on their criminal justice system. He tells Tom Paris and B'Elanna Torres that Benkarans occupy a disproportionate amount of space in Nygean prisons, and are ten times more likely to be executed for their crimes than Nygeans. In particular, Joleg was convicted on circumstantial evidence. Paris tells Neelix from personal experience that in prison, "everyone has a story," and to not put too much stock into what Joleg says. But Neelix reminds him that Joleg is sentenced to die.
In Sickbay the Doctor has applied the nanoprobes to Iko, who has woken up in pain, but much calmer than before. The Doctor observes that Iko is now acting grateful and considerate, a stark reversal of his earlier behavior. Iko complains to the Doctor that he is suffering nausea and that he can't stop thinking about the man he killed. Seven believes his discomfort is a manifestation of guilt. Iko's never felt guilt before, and blames the Doctor for making him feel so horrible. Looking at scans of Iko's brain, the Doctor finds that the nanoprobes have established new neural pathways in his brain. While the Doctor gathers more information about Nygean physiology, Iko tries to make conversation with Seven. She is intrigued when he regains his childhood fascination with stars and constellations.
Meanwhile in the Cargo Bay Neelix teaches Joleg how to play Kadis-Kot. In their conversation Neelix learns that the Nygean legal system is based on a principle called "Vekto Valek K'Vadim" - ancient Nygean for "Favor the Victims" - by which the victim's family dictates the convict's sentence. He also learns that if a defendant is wealthy enough, he can negotiate a monetary settlement with the family rather than serve a sentence. Neelix is appalled and wants to help Joleg, but the prisoner doesn't want to do anything that would imply he's guilty. Instead he asks Neelix simply to transmit a letter to his brother.
The Doctor determines that Iko was born with a congenital brain defect that made him prone to violence and sociopathic behavior, and the nanoprobes have inadvertently repaired it. He informs Janeway of this, and she realizes that Iko's "conscience" has been activated. The Doctor believes Iko is no longer a threat, and Seven notes that by some definitions he is not the same man who committed the murder. They tell a skeptical Yediq that Iko has undergone a fundamental change, and killing him won't accomplish anything. They persuade him to work with Tuvok to draft an appeal and submit it to the authorities on behalf of Iko. Iko doesn't want the appeal though, and tells Seven that he deserves to die. He demands to be returned to his cell, where he asks Neelix to give his meal to another prisoner, Egrid, whom he used to always steal food from.
Later, Janeway and Yediq inform Seven that Iko's appeal was rejected. Seven passionately insists on doing more to help him. Janeway realizes that Seven has an issue with atonement, that perhaps if Iko is found not guilty that she herself will somehow be not guilty for the violent acts she committed as a Borg. Just then the ship is jolted by alien fire. The attack causes a power loss in the Cargo Bay holding the prisoners. Joleg and the other inmates, except for Iko, overpower the guards and escape with weapons. The alien vessel tries to beam over the five Benkaran prisoners, but Voyager fires upon the vessel's transporter array and it retreats.
Meanwhile Tuvok tries to neutralize the prisoners in the ship's corridors, but Joleg takes Yediq hostage and demands a shuttle. Joleg backs into the Cargo Bay and has another prisoner seal the door with a phaser rifle. Joleg pushes Yediq to the floor and prepares to kill him, but Iko stops him, saying, "He's mine." Iko takes the phaser and points it at Yediq while Joleg laughs. But then he hands the phaser to Yediq, who immediately shoots down Joleg and the other prisoner. Yediq realizes that Iko really has changed.
Yediq subsequently uses his influence to convince the family of Iko's victim to hear his appeal. Iko speaks to them on Voyager's viewscreen, saying that he will accept death if it helps them find peace but if they let him live, he'll never hurt anyone again. Meanwhile Neelix tells the re-incarcerated Joleg that he found out the "note" sent to his brother was really meant to help him track down Voyager and attack. Joleg tries again to manipulate Neelix, and the Talaxian leaves disgusted. While Iko and Seven look at constellations in Astrometrics, Janeway arrives and announces that Iko's appeal has been denied. Iko must now be detained again and taken home for execution. Seven is devastated, and for at least a day cannot regenerate. Janeway learns that Seven feels remorseful for having murdered thousands without punishment, but Janeway reminds her that she lost 20 years of her life to the Borg, and that's punishment enough.
The U.S.S. Voyager finds itself under attack by a cloaked vessel. The bridge crew discovers it's an antiquated Klingon battle cruiser, which they can detect with a metaphasic scan. Captain Janeway orders return fire, disabling the vessel's cloak. Janeway hails the damaged ship, telling them to stand down, but Captain Kohlar declares they will not surrender to sworn enemies of the Klingon Empire. Janeway says there's been a misunderstanding since the Klingons and the Federation signed a peace treaty more than 80 years ago. Kohlar does not trust her, so Janeway tells him her Chief Engineer is a Klingon. He wants to meet that Klingon.
Kohlar boards Voyager and meets B'Elanna Torres. He sees that she is pregnant, and asks if the child was conceived during a holy month, which she confirms. Kohlar returns to his ship and tells the other Klingon leaders that the prophecies of the "Scrolls" have come true, and that the "Day of Separation" has arrived.
The Voyager bridge crew realizes the Klingon ship is having a warp core breach. Kohlar requests emergency transport, and all 204 Klingons from the vessel are beamed over into the shuttlebay. Voyager jumps to warp as the Klingon ship explodes. Janeway and Tuvok confront Kohlar with information that he made his ship self-destruct. Kohlar says it was the only way to get them aboard Voyager. He explains that they were following a sacred text that told them to embark on a long journey to find their "Kuvah'Magh" or "Savior." Kohlar believes that savior is the unborn child of B'Elanna Torres.
Janeway briefs the senior staff about the situation and asks them to respect the Klingons and make room for them by having the crew double up on quarters. The Klingons fill the Mess Hall as Neelix provides them meals of gagh, and when a fight breaks out between two of the visitors Harry Kim breaks it up, attracting the attention of a large, lustful Klingon woman. Meanwhile, Torres avoids contact with the Klingons for fear of being ambushed. Some of them start a hunger strike and won't eat until Torres meets with their Council of Elders, so Janeway asks her to cooperate. Torres reluctantly complies, and in the meeting a skeptical elder, T'Greth, realizes she is only half-Klingon and that the baby, with a human father, is also a "mongrel child." Captain Kohlar counters that the signs of the prophecy are there, but T'Greth believes he led them to a false savior.
Later, Kohlar tells Torres that whether or not her baby is the true savior, they must convince his people that she is. He explains that they have been searching for more than a hundred years, and have found nothing but hardship and isolation. He sees Torres and her child as an opportunity to end the wasteful journey. If the Klingons accept her child as their savior, Torres will hold great influence over them and point them toward a home. Torres and Janeway both tell him that they will not deceive his people. So Kohlar suggests that Torres study their scrolls and interpret them in a way that appears consistent with the events of her life, and then they will bring those consistencies to the attention of the council. Otherwise violence could break out.
Torres agrees to help out Kohlar, who makes her realize that the Scrolls can mean anything one wants them to. For example, a "glorious victory against an army of 10,000 warriors" could be interpreted as destroying a Borg vessel, which Torres has helped to do. After spending two days reviewing the Sacred Scrolls, she appears before the Klingon council and tells a spirited story about a heroic encounter with the Hirogen, exaggerating her role in the fight, to the pleasure of the Klingons. She also tells them that Voyager has set course for a planet very much like their homeworld. But T'Greth is still unconvinced, accusing her of saying what Kohlar tells her to. When Torres' husband Tom Paris comes to her defense, T'Greth tests his role in the prophecy by challenging him to a death match. Paris accepts, to Torres' dismay. Janeway refuses to allow such a death match, but at Paris' and Kohlar's urging agrees to a compromise bout where blunted bat'leths would be used and no one would be killed.
Meanwhile, Kim is trying to avoid Ch'Rega, the Klingon woman he restrained earlier and who now wants to mate with him. Neelix helps out by treating Kim with Klingon-style harshness, which causes Ch'Rega to get aroused over the Talaxian instead.
The match between Paris and T'Greth commences in the holodeck. Paris holds his own against his bigger opponent, but he is surprised that T'Greth seems to wear out so quickly. T'Greth collapses, and Kohlar realizes he's come down with the "Nehret," a fatal disease. The Doctor learns that all the Klingons aboard carry the Nehret virus, and have passed it to Torres and her child. Refusing to stay in Sickbay, T'Greth approaches his comrades and declares that since the child has the disease, she cannot be the Kuvah'Magh. They must resume their search, and to do so, they must seize control of Voyager.
The ship arrives at the planet that will serve as the Klingons' new home. Pretending to cooperate with Kohlar, T'Greth asks to beam down as part of the survey mission, rather than to die on Voyager. Kohlar agrees, but T'Greth takes the opportunity, with help from his supporters, to take over the Transporter Room and beam most of the Voyager crewmembers to the surface. Unable to beam out the Bridge crew, the Klingons transport themselves to the Bridge and do battle there with phasers, but T'Greth and his accomplices are eventually knocked out.
T'Greth wakes up in Sickbay and is informed that his illness has been cured - the Doctor has synthesized an antivirus using hybrid stem cells from the unborn mixed-breed baby. T'Greth realizes the child has cured him, and Kohlar declares that she is truly their savior. The Klingons begin to settle on their new homeworld, and Torres accepts a bat'leth from Kohlar, given to him by his great-grandfather, as a gift for the baby. Later, Paris wonders if the child isn't truly the prophesized savior, given the coincidence of the two ships running into each other. Torres doesn't buy it, but she agrees to consider "Kuvah'Magh" as a name for their daughter.
Neelix presents an exotic dinner to Janeway, Chakotay, Paris and Torres, a meal prepared by Seven of Nine who is trying her hand at being a gourmet chef. Suddenly the ship jolts and a graviton surge pulls them toward a swirling funnel, and they wind up in a realm of complete blackness. Then, an alien ship begins firing upon them. As Voyager fires back, a larger ship swoops by and fires at the other ship. Then the second ship fires at Voyager, penetrating their shields, and transports several cargo containers, food, deuterium and other supplies from Voyager to their ship.
Another ship approaches Voyager and an Annarian named General Valen appears on Voyager's viewscreen, welcoming Captain Janeway to "the Void." Coming aboard, Valen tells Janeway that Voyager was sucked into an inert layer of subspace, nine light-years wide, through one of its "funnels." Valen and his ship have been in the Void for five years, and no one has ever found a way to escape from it. In order to survive, the trapped ships compete for resources from new ships that are drawn in.
Torres reports that the anomaly's graviton forces are draining the warp core, and they will run out of power in 10 days. Seven, Tuvok, Paris and Janeway come up with a plan to enter a funnel and jump to warp at exactly the right moment to escape. Implementing their plan, they peer through the eye of a funnel and prepare to jump warp. However, the eye suddenly closes and the funnel shoots Voyager back into the Void. Torres reports that the warp core is now off-line.
Torres thinks she can fix the warp core, but they need the deuterium that was stolen from them or basic systems won't last more than a week. Janeway gives orders to track down the ship that raided them and get back their supplies. They find that ship, but detect no lifesigns on it-apparently it was raided as well. However, one piece left behind-the ship's warp core casing-is composed of tricesium, which can be converted into a power source. Voyager beams the casing over, and when Seven and Torres scan it they find a small alien inside. The timid creature does not speak, and has a leg injury. In Sickbay, the alien won't let the Doctor close enough to treat him, and he eats voraciously. Janeway and Seven wonder why they didn't detect the mysterious being, but decide to make him comfortable until they can find a safe place for him.
Meanwhile, Tuvok and Harry Kim discover that General Valen raided the lifeless ship and now has Voyager's supplies. Janeway contacts Valen and demands the supplies back, but he refuses and the two ships exchange fire. Voyager manages to transport back about half of their stolen resources, and an opportunity presents itself to raid Valen's ship for additional food, but Janeway declines to do that. Later, Tuvok and Chakotay approach Janeway and suggest that the crew may need to be more opportunistic in order to survive in the Void. Janeway points to the Federation Charter as a statement of principles that they should not abandon. Using the Federation model of mutual cooperation, Janeway proposes forming an alliance with other ships to pool resources and devise a way to escape, on the condition that members of the alliance not resort to killing or stealing.
Janeway's first prospective ally is a Jelinian survey ship with a captain named Garon. Skeptical, Garon says he will consider her proposal. Janeway continues to make overtures to a ship of Nygeans and other potential alliance members. Meanwhile, the Doctor realizes the mute creature in his Sickbay loves music, and has named him "Fantome" after "The Phantom of the Opera." Seven gets the idea of trying to communicate with the alien by way of computer-generated tones, and Fantome responds enthusiastically.
A funnel opens in the Void and another ship is pulled in. Two warships approach, including Valen's, and try to attack, but Voyager defends the newcomer. About to lose the battle, Voyager is joined by Garon's ship and forces the raiding vessels to retreat. Garon hails Janeway to accept her offer of an alliance.
With Garon on board, finding new allies becomes easier. Janeway hosts a visit by Commander Bosaal whose ship has technology that could aid in an escape. But he reacts adversely upon seeing Fantome in the Mess Hall, accusing his species of being vermin. Janeway tells Bosaal that they've figured out how to detect the creature's lifesigns and can transport those of his kind off his ship. With that, Bosaal agrees to be an ally.
Torres works with Garon to build a polaron modulator that will help the alliance ships escape the Void, but so far they have failed. Janeway hopes to trade with another ship for a polaron modulator. Meanwhile, Fantome joins others of his kind in learning how to communicate through tones generated by PADDs, creating a musical "conversation" that amazes Janeway. Later, Janeway learns that Bosaal has provided a fully compatible polaron modulator, but pressing him on how he got it, she realizes he stole it from another ship and killed its crew. Enraged, Janeway orders Bosaal off the ship along with the modulator - although the technology would help them escape, she refuses to be accessory to murder. As a result, some of the other ships drop out of the alliance, and Torres has to continue trying to build a modulator from scratch.
Later, one of the remaining allies spies on Bosaal and discovers that he is attempting to form an alliance of his own with Valen and other adversaries, with a plan to attack Voyager. Without the resources to defend themselves, Janeway realizes they need to make an escape attempt right away, even though Torres hasn't had time to test her new modulator. The ship readies its plan with its allies, and Fantome's people - who are native to the Void and live as nomads on ships - want to help out. When a funnel is detected, the alliance ships prepare to go in. Bosaal and his fleet approach and begin firing. Firing back, Voyager manages to penetrate shields on two of the ships and transports Fantome and his friends over. Seconds later Fantome hails Voyager that they have sabotaged Valen's ship; Bosaal's vessel has also been disabled. That gives the four alliances ships time to enter the funnel in a "shield bubble" and jump to warp to enter normal space. The successful allies then wish each other well and go their separate ways.
In a vast alien metropolis on a planet called Quarra, Kathryn Janeway enters a power distribution plant and reports in to a shift supervisor, who takes her to a workstation and explains her task. Janeway has taken a job among a multi-species workforce with no recollection of her previous life as captain of Voyager. When she has trouble working the controls, another worker named Jaffen comes over to help and tries to befriend her. They are chastened for fraternizing by Seven of Nine, who knows herself as "Annika Hansen" (her human name), the new Efficiency Monitor. Jaffen doesn't return to his station until he invites Janeway to go out for a meal after work, but she turns him down.
Meanwhile, Tom Paris-also unaware of who he really is-gets himself hired in a local tavern to wait and bus tables. That night Jaffen is in the tavern telling an anecdote to some friends, and he gets an uproarious laugh from Tuvok, whose behavior is very atypical. Janeway comes in, supposedly to eat alone while she studies manuals, but Jaffen joins her, and he ends up walking her home. They live in the same building, and he invites her to his place; she turns him down.
The next day, Janeway learns that all the workers must periodically receive inoculations to protect them against radiation. As a squeamish Tuvok is getting injected, he has a flashback of himself in his Starfleet uniform, struggling against a Quarren doctor giving him an injection. The strange memory leaves him trembling and perspiring.
All this time Chakotay, Harry Kim and Neelix have been in the Delta Flyer on a trading mission with the Nar Shaddan. When they return, Voyager is not at the rendezvous point. The starship is disabled inside a nebula, and the Doctor is the only crew member on board and is trying to make repairs. When the others find the ship and come aboard, the Doctor explains what happened: Voyager hit a subspace mine which deluged the ship with poisonous tetrion radiation, so Captain Janeway ordered the crew into escape pods, leaving the Doctor in charge of the ship as the Emergency Command Hologram. The Doctor then had to fend off scavengers trying to claim the abandoned vessel, and hid inside the nebula. He since discovered that the subspace mine was a deliberate attempt to disable Voyager. And he hasn't heard a word from the rest of the crew.
At the power plant, Tuvok has another flashback: He and Janeway were brought into a Quarren medical facility where a Dr. Kadan claimed to be treating Janeway for "Dysphoria Syndrome"; when Tuvok demanded her release, Kadan had him restrained and "inoculated." Shaken by this flashback, Tuvok approaches Janeway and says they know each other, that perhaps they met in the hospital, but she has no recollection of a hospital or of knowing him prior to her job. He gives up as Jaffen steps in, who makes dinner plans with Janeway. Meanwhile, Torres is sitting alone in the tavern, and Paris tries to get to know her. He asks to get together with her, but she reveals that she's pregnant, although unmarried, and leaves. The four people aboard Voyager complete repairs and begin searching for their crew. Kim finds them on a Class-M planet less than three days away, and they set course. Janeway and Jaffen have their date, where dinner is a disaster. But it doesn't matter - they fall in love and kiss.
Voyager arrives at Quarra and Chakotay speaks with an ambassador who will not allow him to communicate with his crewmates. The ambassador says they are leading safe, comfortable lives there, and any attempt to disturb them would be met with force. Neelix learns there is a severe labor shortage in the Quarren system, so Chakotay gets the idea of applying for jobs themselves so they can infiltrate the plant where their people are working. Because he has spoken with authorities and could be recognized, Chakotay has the Doctor alter his features to look non-human, and he and Neelix prepare to go to the planet undercover, with subdermal transponders that will allow them to transport through the shield grid.
At the power plant, "Annika Hansen" orders Tuvok to go get the inoculations that he's been neglecting. Tuvok speaks her Borg name - "Seven of Nine" - and tries to mind-meld with her to make her remember herself. But security guards grab him and take the desperate Vulcan away. Chakotay secures a job at the plant and immediately approaches Janeway. She doesn't recognize him, so Chakotay continues the ruse of being a happy new employee. Neelix runs into Paris at the tavern, keeping up the same ruse, unable to jar his friend's memory. After Chakotay meets up with Neelix, they follow Torres in the streets and grab her. Kim beams Neelix and the struggling Torres up to Sickbay, where the Doctor tries to help her. Meanwhile Jaffen asks Janeway to move in with him, and she agrees. Tuvok is in the Quarren hospital where Dr. Kadan tells him he's experiencing "Dysphoria Syndrome" and will feel better after an injection. Chakotay is being pursued by security guards, but Kim can't beam him up because the ship has fallen under attack. The guards chase Chakotay through the facility up to a precipice overlooking the massive city, and he finds himself trapped.
A disguised Chakotay is being pursued by Quarren security officers and is trapped at a forcefield. He smashes a control panel to disable the forcefield, then overpowers the guards and escapes, but not before getting a phaser shot in the arm. Meanwhile, Harry Kim and the Doctor are in command of Voyager as it is being fired upon by Quarren patrol ships. They disable the first two ships, but five more approach and they are forced to retreat. The injured Chakotay enters the tavern where a brainwashed Janeway has just decided to move in with her new boyfriend, Jaffen.
A Quarren investigator named Yerid enters the tavern inquiring about two people who disappeared earlier that evening-named B'Elanna and Neelix. The waiter, Tom Paris, points him to Chakotay, but he's already disappeared. In the Quarren hospital, Dr. Kadan orders a skeptical Dr. Ravok to do a memory sequencing treatment on Tuvok. Meanwhile in the power plant, Seven of Nine is on the job and has a flashback of life on a Borg cube. Connecting the flashback to her encounter with Tuvok earlier, she goes to her Supervisor's office and asks about him. Yerid arrives to inquire about the two missing employees, saying he believes that Amal Kotay-Chakotay's assumed identity-is responsible for their disappearance.
Janeway moves her things to Jaffen's apartment, but when she returns to her old place she finds Chakotay hiding out there. He tells her that B'Elanna and other people in the city were brought to the planet against their will and made to forget their real lives, and he's trying to help them. Janeway reluctantly lets him stay, and decides to do something about his injury. Voyager, meanwhile, has hidden in a moon's crater to make repairs and to treat Torres for her altered memory. Neelix takes Torres to her quarters to re-introduce her to her real life, and she is surprised to learn that the waiter from the tavern is her husband. At the plant, Seven catches Janeway taking a dermal regenerator, but she promises to return it. Seven is sidetracked when she has an opportunity to enter the Supervisor's office and use his console; she learns that Tuvok has accessed numerous employee files including Janeway's, B'Elanna's, and her own. Janeway returns to Chakotay to heal his injury, and he reveals that he's from a ship called Voyager. Chakotay observes that she seems happy in her job and her life, but she seems capable of so much more. Janeway responds that she wouldn't want more responsibility. Chakotay is contacted by Voyager through his subdermal transponder, and they inform him that the ship is two days away but need the planet's shield grid disabled so they can transport the crew members back. Chakotay tells Janeway that she's the captain of that ship, but she has a hard time believing him. To prove himself, he takes the dermal regenerator and undoes the alterations made to his face, revealing that he is the same race as she. He tells her they are also friends.
Janeway tells Jaffen the story she just heard, but he thinks Chakotay is trying to manipulate her with promises of a better life. Meanwhile Chakotay is found by Yerid and is taken in for questioning. Chakotay tells him they are both investigating disappearances, and has questions of his own. Just then Dr. Ravok enters with orders to transfer Chakotay to Neuropathology to be treated for mental illness. As he's taken away, Chakotay tells Yerid the truth about himself and his abducted crewmates.
On Voyager, Kim and the Doctor are discussing tactics and arguing over whether the Doctor should remain a Command hologram, when they are hailed by Chakotay. He says he's almost ready to shut down the shield grid, and gives instructions on where and when the ship should enter orbit. They don't know that Chakotay is being subjected to a mind control device and is sending them into a trap.
At the tavern, Seven meets discreetly with Yerid to share her findings that more than a hundred employees-most of the same species-began work on the same day, which is unusual during a labor shortage. Also, they were all processed through the Neuropathology division, including herself, which she doesn't remember. Seven wants Yerid to interview Tuvok in the hospital, but Yerid reveals he was relieved of duty that morning. So Seven goes to the hospital herself and visits with Dr. Ravoc, reporting that she's been having "disturbing thoughts." Ravoc looks up her file and sees she was previously treated for Dysphoria Syndrome. She asks to speak to an expert on the condition, so Ravoc steps out to get Dr. Kadan. She takes that opportunity to use his computer. Meanwhile, Yerid contacts Janeway and asks to know everything Chakotay told her.
At the hospital, Kadan is enraged that Ravoc allowed Seven to access restricted files and leave. Ravoc is suspicious that an apparent "outbreak" of Dysphoria Syndrome occurred under Kadan's watch, and realizes that he had made false diagnoses on patients, altered their memories and sent them to work at the power plant. Kadan admits it's true, but claims it was to cure the labor shortage and improve the patients' lives. Ravoc threatens to report him, but Kadan says the authorities are behind him. Meanwhile, Paris harbors Seven, Janeway, Jaffen and Yerid at the tavern, who are collaborating about Chakotay's story and how to prove it. Janeway and Jaffen go to the power plant to use a subspace transponder to contact Voyager, while Seven and Yerid return to the hospital to help Chakotay and Tuvok.
With Jaffen's help, Janeway succeeds in hailing Voyager, where she sees B'Elanna in uniform and hears Kim call her "captain." B'Elanna asks her to find a way to shut down main power so the shield grid will be disabled. Just then Voyager comes under attack by three ships, and Janeway is surrounded by security guards. Jaffen helps her evade them, then she works the computer to make it think the reactor core is overloading so it'll automatically shut down main power. Meanwhile in the hospital, Seven and Yerid point a weapon at Kadan to force him to release Chakotay and Tuvok from the mind control devices. On Voyager, Kim gets the idea to use three escape pods as armed decoys to disable the attacking ships. They succeed, and B'Elanna gets the transporters back on line. Janeway's own plan works, and power goes out all over the city. With the shield grid down, Voyager beams up all of its crew members. The Doctor treats them and they recover, but in the meantime he, Kim and Neelix confer with Yerid and the Quarren Ambassador about undoing the conspiracy, with a promise that all of Kadan's "patients" will be treated and repatriated. Janeway says a final good-bye to Jaffen, then resumes her role as captain and takes Voyager on its way.
Seven of Nine programs Holodeck 2 to be a rustic cabin where she practices the piano to the steady beat of a metronome, with her hair down and her Borg implants gone. Later, she attends a simulation of B'Elanna Torres' baby shower, where she again appears fully human and interacts with holo-crewmembers more freely than usual. She even makes a toast to the new baby. Just then the real crew on the Bridge detects mysterious energy discharges ahead, and Seven gets called to Astrometrics. Captain Janeway, Tuvok and Tom Paris meet her there, but Seven cannot find the source of the discharges. Opting not to alter course, Janeway turns her attention to the actual baby shower the crew will surprise Torres with later that day. Janeway asks Seven to be there, but she makes an excuse not to.
Instead, Seven returns to the holodeck where she creates new quarters for herself, and a holo-Neelix gives her advice on how to decorate the empty space. A holo-Chakotay arrives with a housewarming gift, a Native American dreamcatcher. Seven invites him back the following night for dinner.
At Seven's weekly physical in Sickbay, the Doctor tells her that Tom and B'Elanna missed her at the baby shower. Noting that her shoulder implant is out of alignment and her electrolyte levels are down, the Doctor learns that Seven missed her regeneration cycle. She claims it was because she was conducting "research" that had something to do with her personal life, which surprises the Doctor. Just then Voyager is rocked by another energy discharge, which produces a shockwave that then hits the ship violently and damages its warp drive. In Astrometrics, Seven discovers the explosion came from a subspace warhead that destroyed an unmanned probe. Since warp drive is down until repairs are complete, Janeway asks Seven to find a way to detect the warheads before they emerge from subspace, to give the crew a few seconds' warning.
Later, Icheb comes to Astrometrics to relieve Seven, because the Doctor wants her to spend more time regenerating. But instead of going into her alcove, she takes a belated baby shower gift to Torres in Engineering, and tries awkwardly to engage in small-talk. Then she modifies her holodeck program to fully decorate her quarters and put herself in an alluring dress for her date with holo-Chakotay. They prepare dinner together, and the mood gets increasingly romantic until they kiss. Suddenly Seven is distracted by a shrill noise, but she ignores it as she embraces her new simulated boyfriend.
The next morning Seven has disturbing dreams where she sees herself as a drone and her metronome appears as Borg technology. She wakes up when the real Chakotay summons her, which is odd because she's next to the holo-Chakotay. She arrives in Astrometrics where Icheb has picked up a warning beacon revealing that Voyager has entered a munitions testing ground. Chakotay is concerned that Seven was late for her duty shift, but she denies being distracted.
Later Seven is back in Holodeck 2 playing the piano for holo-Chakotay to the beat of the metronome. He's impressed by her flawless technique, but then he stops the metronome and tells her to play with more feeling. She's frustrated and anxious at first, but gradually she's able to play more from the heart, without needing to be perfect. Just then three alien missiles emerge from subspace and destroy a target probe, sending out shockwaves that rock Voyager. The real Chakotay calls on Seven for her sensor calibrations, but she needs a moment to return to her station. While the ship shakes hard, Seven gives Paris coordinates for other warheads about to emerge, but they turn out to be wrong. She corrects herself, and Paris is able to re-orient the ship to withstand the next shockwave.
In her Ready Room, Janeway chides Seven for being late with her sensor calibrations and for being away from her post, and asks why she's logged so much time in Holodeck 2. Seven tells a direct lie-that she's been running a simulation to improve ship systems-and apologizes for dividing her time while the ship is on alert. Janeway accepts her story and her apology, and looks forward to seeing her simulations. Seven returns to Astrometrics, where Icheb detects a strange attitude from her. Admitting she's been negligent, Seven leaves again to go "correct an error."
In the holodeck, Seven activates the Chakotay simulation again to end her relationship with him. Holo-Chakotay argues that every time she moves closer to her emotions, she backs away again, afraid that embracing her humanity will make her weak. She argues back that the ship needs her, but then she hears the mysterious high-pitched noise again, this time piercing through her head. She summons Sickbay and faints. The Doctor arrives and finds her going into neural shock. Seven wakes up in Sickbay, where the Doctor reveals that her cortical node began to shut down, but he managed to stabilize it. He asks what she was doing before she collapsed. She admits that she's been conducting simulations to explore different aspects of her humanity, such as social activities and intimate relations. She reveals that since Unimatrix Zero was destroyed, she's been trying to re-create some of the experiences she had there and feel some of those emotions again. But she plans to delete her holodeck programs because her "personal life" has distracted her from performing her duties efficiently.
Torres succeeds in getting engines back on-line, and Voyager jumps to warp. But then a subspace warhead locks onto the warp signature and targets the ship. The missile neutralizes a spread of photon torpedoes and continues closing in. Seven scans the warhead's detonator in an attempt to disarm it, but is unable to. Then she believes she can extract the detonator by transporting it out, but only at very close range. With no time to spare, she accomplishes the transport and the missile breaks apart harmlessly.
Later, the Doctor approaches Seven with bad news: Her cortical node did not malfunction, but in fact was designed to shut down her higher brain functions when she achieves a certain level of emotional stimulation-not surprising for a Borg implant. The Doctor believes he can reconfigure the node so she can continue her simulations, but it would be a difficult and lengthy process. Seven declines the procedure, saying that she's experienced enough "humanity" for the time being and the "failsafe" device will ensure that she's no longer distracted. The next day Chakotay invites Seven to a get-together in the Mess Hall, but she turns him down. He suggests that a little more socializing might do her good.
Captain Janeway is caught by surprise when she is paid a visit by Q and his son, Q ("Q2"). She last saw the young Q as an infant four years ago, but he already looks and acts like an adolescent, and his father wants to leave him on Voyager to learn about humanity. The crew quickly learns that the boy is trouble, being as bored and out-of-control as any teenager but with omnipotent powers. Q2 throws a party around the warp core, he makes Seven of Nine's clothes disappear, and he gives the computer a rebellious personality. Neelix is shocked to find him initiating a war between two cultures, and when he tries to talk him into using his powers more constructively, Q2 takes his vocal chords away. Then Q2 lures three Borg Cubes to attack Voyager, putting the crew in danger.
The father Q then shows up, sets things back to normal and speaks privately with Janeway. He tells her that his son was supposed to inspire peace and compassion, but instead has brought chaos to the universe, so the Continuum is hounding him to straighten the boy out. He was hoping that Janeway's "Starfleet ideals" would rub off on him, but she tells Q to act more like a parent and spend time with him. Q loves the idea, kisses her on the lips and disappears. Minutes later, Q appears again in Janeway's bubble bath, telling her he just spent years with his son smothering him with attention, and things have only gotten worse. Janeway tells Q that he needs to make his son understand that there are consequences to his actions. In response, Q turns his son into an Oprelian amoeba, and when he restores him, tells the boy he will be sentenced by the Continuum to an eternity as an amoeba unless he becomes an upstanding citizen of the cosmos. He gives Q2 one week to change his ways, and strips him of his powers.
Forced into playing "mommy" to the now-mortal boy, Janeway assigns Q2 quarters and devises a strict curriculum for him with crewmates as his instructors. For instance, Chakotay runs a diplomacy scenario on the holodeck where Q2 is instructed to settle a mining dispute among several races. But when Chakotay leaves the room, Q2 alters the aliens' personalities to assure speedy success. He is also assigned to write a historical essay on the Q Continuum, but Q2 manipulates Icheb into writing it for him. Janeway tells Q2 that she knows he's been cheating, and orders him to his room to wait for his father to return. Not wanting to live as an amoeba, Q2 explains that it's not easy to live up to his father's expectations and tells her she's his only hope. Janeway agrees to give him one more chance.
Janeway and the Voyager crew become impressed with Q2's determination to improve himself. Janeway is also pleased with Q2's new essay on the Q Continuum. She rewards Q2 by allowing him to go with Icheb on his piloting lesson with Lt. Paris. After helping Icheb navigate the Delta Flyer through an asteroid field, Paris lets Q2 take a "turn at the wheel." Q2's nervousness gives way to a sense of adventure, and he and Icheb become friends. Meanwhile, Q returns to Voyager to check up on his son's progress. Janeway has Q2 read his essay to his father, but Q is not at all impressed, hurting his son's feelings. When Q2 leaves the room, Q tells Janeway that the boy needs to demonstrate nothing less than exemplary "Q-ness." Janeway prods him to explain what that is, but he just says he knows it when he sees it, and an essay is not it, and disappears. Janeway visits Q2 to console him, telling him that if the Continuum won't take him back, she'll ask them to let him stay on Voyager as a human. But Q2 doesn't want to be human - he wants to be a Q, like his father.
Later, Q2 convinces Icheb to help him repair an ion imbalance on the Delta Flyer to surprise Paris. After making the repair, Q2 launches the Flyer without permission, telling Icheb he knows how to open a spatial flexure to another system. Icheb strongly objects, but Q2 wants to hide from his father. He breaks free of Voyager and jumps through the rift to the Clevari system. The Flyer is met by a Chokuzan ship, whose commander accuses them of trespassing and demands their surrender. Q2 fires on the ship and tries to escape into another flexure, but the Chokuzans fire back, and a bolt of energy knocks Icheb out. Q2 returns to Voyager to bring Icheb to Sickbay, but the Doctor can't treat him unless he knows more about the weapon that struck him. Q shows up again, and Q2 pleads with him to save his friend's life, but Q refuses, telling the boy he has to face the consequences of his actions.
To save Icheb, Q2 agrees to return with Janeway to the ship that he attacked. Q2 apologizes to the ship's commander and asks for his help, but when the commander threatens to hold Janeway accountable for the boy's actions, Q2 objects and insists on accepting punishment, even if it's torture or execution. The Chokuzan commander laughs and reveals himself to be Q in disguise. All along the Chokuzan incident was a test, which Q2 passed with flying colors. After Q assures Janeway that Icheb will make a miraculous recovery, the two Q's and Janeway appear before a tribunal of Q-Judges. Although Q argues that his son was willing to sacrifice himself to save another, the judges rule that Q2 has not made sufficient progress and must suffer the fate of staying human. Q is outraged, and disappears with the judges. Q2 dejectedly returns to Voyager, where he asks if he can stay and continue his training, feeling he still has a lot to prove to Janeway. But Q comes back and explains that he told the judges he wouldn't stay in the Continuum without his son, and claims they "begged" him not to leave. In fact, Q2's powers have already been restored. Q2 fills Janeway's ready room with flowers to thank her, and leaves on Q's promise to be a better father. Q reveals to Janeway that he had to agree to one minor condition eternal custody of the child. In thanks, Q gives Janeway data on a shortcut home, but he won't take Voyager all the way because it would be a bad example for his son.
While the Doctor creates a working draft of his new holonovel, the U.S.S. Voyager prepares for "Operation Watson," whereby the ship will establish a two-way com link with Starfleet using a tachyon beam bounced off a quantum singularity. Reginald Barclay and Admiral Paris from the Pathfinder project on Earth appear on the Astrometrics domescreen and tell Captain Janeway that the com link will only work for only 11 minutes a day. Three people can talk to their loved ones in the Alpha Quadrant for three minutes per day, so Neelix has the crew draw numbered isolinear chips. The Doctor draws number one, so he contacts a well-known Bolian publisher on Earth - Ardon Broht of Broht & Forrester - to discuss the holonovel which he had previously transmitted to him. Broht raves about the piece and wants to distribute it right away, but the Doctor insists on making revisions first. Later, the Doctor brags to Lt. Tom Paris about his conversation with the publisher, which raises Paris' curiosity about the hologram's opus. He convinces the Doctor to let him experience the holonovel, which he learns is titled "Photons Be Free."
Paris finds himself in the role of the Emergency Medical Hologram (EMH) aboard the "Starship Vortex," and he sees that the first chapter starts out almost identically to the Doctor's own experience of being first activated. The other characters resemble the real crew, but altered slightly in their appearance - for instance, Chakotay is a Bajoran. When Paris, as the Doctor, decides to treat a critical patient ahead of a bridge officer, Captain "Jenkins" (Janeway with black hair) enters Sickbay and kills the dying crewman, so that the bridge officer can now be treated. Shocked at how the crew is portrayed, Paris tells B'Elanna Torres and Harry Kim about it, and they think he's overreacting. So Paris tells his crewmates to try it out themselves.
Torres experiences for herself how badly the "Vortex" EMH gets treated by the holo-crew, especially her own look-alike; Neelix, in the same role, is scolded and threatened by Captain Jenkins; and Kim becomes part of an escape plan with help from "Three of Eight." Finally, Janeway experiences the final chapter of the holonovel, where the EMH is brutally decompiled. She immediately orders the Doctor to report to her Ready Room.
The Doctor defends the piece, claiming it's a work of fiction with an important message. Janeway wonders if the Doctor sees himself as oppressed, but he explains he intended to draw attention to the plight of his "brothers" in the Alpha Quadrant, other EMH Mark Ones like him who have been condemned to menial tasks. Janeway asks him to consider how his writing makes his friends feel, but he won't compromise on his self-expression. When he returns to the holodeck to make final revisions, he finds the program altered with a holo-Paris as the narrator, and the story about the assistant to the Chief Medical Officer who has to learn to tolerate his overbearing manner and obnoxious behavior. Incensed, the Doctor confronts Paris about distorting his work. Paris assures him he kept the original intact, but was simply trying to make a point that someone running a program like that would think the characters were based on the real people. But what bothers Paris most is that the immature, self-indulgent character that bears his likeness apparently reveals what the Doctor really thinks of him.
Neelix talks to the Doctor and helps him realize that by publishing his program, he may hurt the people he cares about, and he can make adjustments so that it's not so obviously based on Voyager without sacrificing his theme. But a rewrite will take weeks and the publisher is expecting a final draft tomorrow. Neelix tells the Doctor to give the publisher a call, and hands him his numbered chip. Broht is not happy to hear that the work will be delayed, but the crew is grateful to the Doctor for taking their feelings into account, and Paris agrees to assist with the revisions.
Meanwhile, members of the crew get to talk to family members they haven't seen in years. Kim's parents wonder when he's getting a promotion, and offer to write Captain Janeway a letter, which Harry strongly discourages. Torres begrudgingly agrees to talk to her father, who abandoned her when she was a child; during their awkward conversation, John Torres expresses regret and hopes they can get to know each other again. Even Seven of Nine uses her com time to contact her nearest living relative, an aunt on Earth; Irene Hansen tells Seven about how she was as a child, and calls her Annika.
Janeway receives an urgent message from Admiral Paris: He just learned from Barclay that the Doctor's holo-novel has been distributed and is being played in thousands of holosuites. The Doctor contacts Broht demanding a recall and a public apology, but Broht refuses. Janeway points out that authors have rights, but Broht responds that under Federation law, holograms have no rights.
After discussing legal options with Tuvok, Janeway decides to request a hearing to seek the same rights for the Doctor as any flesh-and-blood person. A Federation Arbitrator hears arguments from Broht and from the Voyager crew, who testify that the Doctor has demonstrated the traits of a "person" such as creativity, ambition, friendship and fallibility. After several days of arguments and deliberations, the Arbitrator announces he is not prepared to rule that the Doctor is a "person" under the law, but he is willing to extend the definition of "artist" to include the Doctor; therefore he orders all copies of the holo-novel recalled immediately. The Doctor apologizes to Janeway for the damage that's been done, but the crew encourages him to continue revising his work and to find a new publisher. Four months later, on an asteroid in the Alpha Quadrant where hundreds of EMH Mark Ones (all identical to the Doctor) are now mining dilithium, word gets around among the holograms that there is a very provocative new program in the holo-lab called "Photons Be Free."
Now that the U.S.S. Voyager has established two-way communications with Starfleet, Captain Janeway receives her first official assignment in seven years: Locate and retrieve the Friendship 1, a probe launched from Earth in 2067 with a message of peace to other worlds. Contact was lost 130 years ago, but its known trajectory would place it in the Delta Quadrant near Voyager's current position. After five days of searching, the probe is detected on a planet darkened by a nuclear winter caused by antimatter radiation.
An away team consisting of Tom Paris, Harry Kim, Chakotay, Neelix and Lt. Joe Carey take the Delta Flyer to the planet, who go searching for the probe wearing environmental suits. While Paris, Neelix and Carey follow their tricorder readings into a cavern, Chakotay and Kim are surprised to find a field of missile silos containing active warheads. Paris, Neelix and Carey see evidence that the cavern is inhabited, but sensors have detected no lifesigns. They find a piece of debris labelled "Friendship 1" and prepare to transport it to the Flyer, but then are suddenly surrounded by armed aliens who are cloaked in heavy robes and breathing equipment. Meanwhile Chakotay and Kim discover the Flyer has been invaded by one of the planet's inhabitants, who attacks them but then gets knocked out by Chakotay's phaser. Then antimatter weapons start rocking the Flyer, so Chakotay is forced to fly it back to Voyager, leaving the others behind. In the cavern, the native people show themselves to be highly malformed and mottled from radiation exposure, and their leader, Verin, is very hostile to the away team. When Verin learns they're here to retrieve their probe, he accuses them of causing his people's suffering.
Verin contacts Voyager and tells Janeway he's taken her crewmen hostage, demanding the relocation of his people to another planet starting in three hours. Janeway confers with the Doctor, who has examined the unconscious alien Chakotay brought back, and learns that his tissues are saturated with antimatter radiation, explaining why no lifesigns were detected on the planet. The Doctor wakes the alien, named Otrin, who reveals that his planet's devastation was caused by an antimatter containment failure. And he blames the human race for it because until the Friendship 1 arrived and introduced that technology, his people had never conceived of anything like antimatter. After decades of suffering, they came to the conclusion that humans intended to contaminate their world so they could eventually come and conquer it.
Tuvok locates a Class-M planet 132 light-years away, and determines it would take almost three years to completely relocate all 5500 of the aliens. Meanwhile Seven of Nine extracts nanoprobes from her bloodstream so the Doctor can reprogram them to cure Otrin of his radiation sickness, and Janeway asks Otrin to elaborate on his efforts to neutralize the planet's radiation. On the surface, Neelix tries to tell Verin that humans are not so bad and never meant to harm his people, but he remains unconvinced. Janeway later contacts Verin and tells him that relocation is impractical, offering an alternative: help Otrin carry out his theories on how to counteract the radiation. Verin won't budge on his demands, so Janeway asks to exchange a supply of food and medicine for one of the hostages. Verin picks out Carey and tells him to set up the transport enhancers. Just before Carey is beamed out, Verin shoots him in the heart and he arrives in Sickbay dead.
Janeway tells Verin she will start evacuating his people in an hour, but then she calls Tuvok and Chakotay into a meeting. In Sickbay, Otrin is getting much better after his nanoprobe treatment, and hopes that Voyager can heal all his people. But Seven points out that Verin has refused their help, and suggests to Otrin that he would be a better leader than Verin. Meanwhile Paris helps a woman on the surface deliver a baby, which arrives stillborn, but Paris is able to bring it to life. Just then a patrol captures another Voyager crewmember, Tuvok, making Verin believe he has another hostage. But it turns out one of the alien guards is the Doctor in disguise, and he helps Tuvok overpower the captors. The hostages can now beam out, but before leaving, Paris tells the new mother the baby won't survive without further treatment, so she lets him take her son to Voyager.
Once the baby is stabilized, Janeway plans to send him back along with some food and medical supplies, but then leave. Paris and Neelix appeal to the Captain to help these people in spite of their refusal to cooperate. So Janeway and Seven work with Otrin to develop a plan to neutralize the planet's radiation with an isolitic chain reaction, using photon torpedoes to deliver the catalytic agent.
Otrin brings the now-healthy baby back to the surface and confronts Verin to accept Voyager's help and begin trusting them. Meanwhile the ship enters the planet's atmosphere to detonate the charges that will counteract the radiation. When the ground begins to shake, Verin arms an antimatter missile and prepares to launch it at Voyager. But his own lieutenants and the grateful mother aim weapons at him to prevent him from ruining their only chance for survival. Verin realizes Otrin is in command now. Just then a child runs in and urges everyone to come outside. They see that sunlight is starting to break through the dark clouds, for the first time in decades. Voyager retrieves the Friendship 1 and resumes course for the Alpha Quadrant, but the success of their mission cost them the life of a crew member.
While travelling in a shuttle to the planet Ledos for a conference on Warp Field Dynamics, Chakotay and Seven of Nine take a detour to admire the natural landscape of one of the planet's subcontinents, and in doing so they scrape a mysterious energy barrier that starts to break the shuttle apart. Seven uses phasers to open a rift in the barrier, and they beam to the surface before the shuttle explodes. They find themselves stranded in a lush jungle, and in spite of Chakotay's leg injury, set out to find the shuttle debris in hopes of constructing a beacon to send a distress signal.
Meanwhile Tom Paris flies the Delta Flyer somewhat recklessly through the bustling Ledosian spaceport, and learns from the Port Authority that he has committed a piloting violation. Captain Janeway later informs Paris that his penalty, under local law, is to take a three-day course in flight safety, and since she has decided to grant the crew shore leave on the planet, he'll have time to complete it much to his chagrin.
On the surface, Chakotay and Seven discover a tribe of primitive humanoids living in the jungle. Agreeing they should avoid contact with them, Chakotay - who is developing an infection - rests while Seven continues searching for debris. While she's away, three native men sneak up on Chakotay. Just then Seven finds a working piece of the shuttle and summons Chakotay, and the natives, startled by her disembodied voice, grab his combadge and destroy it. Seven returns and finds that Chakotay has been taken into a cave. It turns out the natives are friendly, and they are treating his wound. Chakotay talks Seven into staying the night, but she is uncomfortable with the degree of fascination the unspeaking natives have for them, especially an adolescent girl who is intrigued by her Borg implants.
As Harry Kim, Neelix and B'Elanna Torres prepare to beam down to the planet for shore leave, they tease Paris for having to attend "pilot school." Paris is confident he can skip right to the test and join them in a couple of hours, but then the flying instructor, Mr. Kleg, beams aboard and makes it clear he intends to take as much time with Paris as he deems necessary.
The next morning, Chakotay begins to learn the natives' sign language as he draws a map in the ground to get his bearings. Seven tells him she can construct a beacon by connecting the components she found with the shuttle's deflector, which she has detected six kilometers away. Since he's still injured, Chakotay suggests letting one of the locals guide her, but she won't because she's still trying to limit contact with them. As she makes her way through the dense jungle brush, she takes a fall and loses her tricorders into a crevice, and has to proceed without it. Meanwhile, Chakotay makes a startling discovery: the native men have started painting tattoos on their foreheads that look like his.
That night, Seven has to endure cold and rain, but then the adolescent girl shows up and brings her a blanket. The girl builds a fire and offers Seven food, which she turns down. The next morning Seven finally accepts the food, and allows the girl to guide her through the jungle. Along the way, though, the girl insists they stop and admire the view of spectacular triple waterfall. Back at the encampment, Chakotay is worried about Seven, and when he tries to communicate that he needs help to find his friend, a native man misunderstands him and brings out a woman who has strapped a small piece of shuttle debris to her forehead, to emulate Seven. Chakotay finds out they have retrieved several pieces of technology from the shuttle, and gets them to lead him to where they found it. Meanwhile, Seven and the girl find the shuttle deflector.
On Voyager, Tuvok reports to Janeway that Chakotay and Seven have failed to report in, and they never showed up at the conference. Tuvok and Kim have located a wing from their shuttle resting on top of the energy barrier surrounding the southern subcontinent, which means the missing crewmen are probably there, but they cannot be sure because the barrier is deflecting all their scans. Janeway contacts the Ledosian Ambassador, who informs her that the barrier shields the territory of the indigenous Ventu, and it was erected centuries ago by aliens to protect the Ventu from having their culture destroyed by the Ledosians' own unenlightened ancestors. But the technology is a mystery to them, so they can't lower the barrier, and since it's generated from the inside, the Ambassador holds no hope that the crewman, if alive, can ever get out.
On the surface, Chakotay meets up with Seven, and they recruit help from the Ventu men to move the deflector to a spot where Seven believes she can generate a deflector beam to temporarily neutralize the barrier, thus allowing them to escape and Voyager to beam away all their technology. Meanwhile Voyager is attempting to penetrate the energy barrier with phasers, but feedback from the barrier is interfering with the ship's systems, forcing them to cease. A short time later, though, the crew learns the barrier is being deactivated from the inside. Seven has successfully generated a dampening field, but the Ventu girl gets too close to the deflector and receives a serious shock. When Janeway's voice comes through telling the crewmen to stand by for transport, Seven reports that she needs to remain behind to treat an injury.
After the Ventu girl recovers, Seven says goodbye and accepts the girl's blanket as a gift. Just then she hears voices approaching - a Ledosian expedition has arrived to conduct scans and evaluate the habitat for development. Barus, the expedition leader, tells Seven she did the Ventu a great favor by lowering the barrier, because now they can benefit from education and technology. On board Voyager, Seven, Chakotay and Janeway debate whether or not the Ventu would be better off losing their isolation, but decide their unique way of life is worth preserving. When Janeway announces to the Ledosian Ambassador her intention to restore the barrier, he protests, but says he will remove his people from the territory. However, when Voyager tries to beam up the deflector assembly, a Ledosian vessel fires and knocks out their transporters. Janeway then contacts Paris, who is still in the Delta Flyer maneuvering through a training course with Mr. Kleg, and gives him encrypted orders. Over Kleg's objections, Paris suddenly peels away from the course and rushes to the planet. He beams up the expedition team, then finds the deflector and vaporizes it with phaser fire, and zooms away a split second before the energy barrier goes back up. Mr. Kleg tells Paris he has failed the course.
Back on board, Seven tells Chakotay she's concerned that the Ledosians may have scanned her deflector modifications and could find a way to remove the barrier themselves. She realizes if she hadn't made those modifications, the Ventu would be safe, but they would still be stranded. All she and Chakotay are sure of is that they're glad to be back on Voyager.
Neelix is hosting a party to celebrate First Contact Day, the anniversary of the Vulcans' arrival on Earth, when Chakotay interrupts with news that sensors have detected Talaxian lifesigns a few light-years away. The U.S.S. Voyager follows the readings to an asteroid field, so Tom Paris, Tuvok and Neelix take the Delta Flyer to track down the Talaxians. They discover their lifesigns inside a large asteroid, but then an explosion forces the Flyer to crash-land on that asteroid.
Neelix regains consciousness to find a pretty, widowed Talaxian woman named Dexa treating his injuries. She tells him his friends are safe, and that the explosion came from miners who are using charges to break apart asteroids for their mineral resources. Dexa wonders why Neelix is living with aliens, and keeps him locked behind a forcefield. Meanwhile on Voyager, the crew is preparing a rescue mission when Commander Nocona, the leader of the miners, hails them and explains that a mining operation is in progress. He warns Captain Janeway to stay out of the field and says his people will search for the missing crewmembers.
Neelix is visited again by Dexa, this time with Talaxian council regent Oxilon, who tells him he's free to go. While they're willing to let Neelix stay awhile, they want his alien friends to leave as soon as possible, prompting Neelix to take his leave as well. As Dexa escorts him back to the Delta Flyer, Neelix learns that 500 Talaxians live inside the asteroid, which they excavated and developed using technology from their disassembled ships. Neelix rejoins Paris and Tuvok in the Delta Flyer, feeling let down that the encounter with his people fell short of his expectations. As repairs are being completed, an intruder alert reveals that Brax, Dexa's young son, has snuck on board. When Neelix takes the boy back to his mother, he finds her and Oxilon in a confrontation with the miners. Nocona is ordering the Talaxians to evacuate the asteroid so it can be demolished. Dexa stands up to him in defense of her home, and he pushes her aside. In response Brax throws a rock at Nocona, and when the miners attempt to grab the boy Neelix defends him and gets into an altercation with the miners. They reach a standoff, so the miners give the Talaxians three days and leave.
Oxilon is worried that the fight may have made things worse, but Dexa suggests it's time to defend themselves rather than run away. Neelix offers to help out by asking Captain Janeway to negotiate with the miners, and asks Dexa, Oxilon and Brax to visit Voyager. Neelix gives Dexa and Brax a tour of the ship, and while Naomi takes Brax on a holodeck adventure, Neelix and Dexa have dinner together. He learns that her people - refugees from the Haakonian takeover of Talax - first settled on a planet called Phanos where they were restricted to a very small area. When her husband attempted to farm outside their allowed zone, he was killed by a government patrol. Then they came to the asteroid, where they thought they wouldn't be bothered. Neelix reassures her there's still hope, and the attraction between them grows.
The next day Janeway leads discussions between Nocona and Oxilon, but the miners won't compromise except to extend their deadline for evacuation. After the failed negotiation, Janeway agrees to ferry the homesteaders and their supplies to the nearest M-Class planet. Concerned for their safety, Neelix asks Tuvok for advice on how to devise a defense strategy for the Talaxians' new home. Tuvok proposes that their current home could be defended by a shield perimeter, but with the miners monitoring the asteroid they would need competent leadership to defend against a pre-emptive attack. Tuvok suggests to Neelix that he could be that leader.
With Janeway's blessing, Neelix takes his own ship to the asteroid and proposes to the homesteaders a plan to establish a shield grid, by using their one remaining ship to implant 16 forcefield emitters into the asteroid's surface. The miners will attack, so Neelix will provide cover from his own ship. Oxilon protests that people will get hurt, but Neelix counters that their home is worth defending, and Dexa agrees. As the Talaxians prepare for the operation, Neelix and Dexa share a passionate kiss.
Oxilon pilots the ship that fires the emitters into the asteroid, and as he gets into position to plant the last one, the miners intercept and attack. After Neelix retaliates, the miners start dropping charges to demolish the asteroid. He manages to neutralize one of their charges, but then the miners knock out his weapons, so when the next charge is dropped Neelix attempts to collide with it. But then the Delta Flyer arrives and obliterates the explosive, saving Neelix's life. Janeway contacts him and says they just came to help a friend in distress. The final emitter is planted and Dexa activates the shield, successfully repelling the miners' attacks.
As Neelix says goodbye to his new friends, Brax asks him to stay. After returning to Voyager, and especially after realizing that Naomi is growing up, Neelix finds himself in a dilemma. When he tries to talk to Janeway about it, she offers him a chance to serve as Starfleet's permanent ambassador in the Delta Quadrant. He accepts, and after a touching send-off by the crew, leaves Voyager for good to join his people, and become a family with Dexa and Brax.
Captain Janeway and the Doctor run into a problem as they travel back from a medical symposium on the Delta Flyer. When Janeway returns to the U.S.S. Voyager, she tells Chakotay that they encountered a race called the R'Kaal who have outlawed conventional warp travel through their territory, and insist on punishing Voyager by dismantling the ship. Janeway says she agreed to surrender their warp core in exchange for letting the crew settle on an M-Class planet. Chakotay is concerned that the captain is giving in so easily, but Janeway insists she's tired of continually risking her people on a slim chance of making it home, and orders Chakotay to set a course for the planet.
Janeway then asks Torres to modify the Flyer's tractor beam so that if the warp core is ejected, it can be safely towed at warp speed. Chakotay learns of this order, and tries to find out from Janeway what's really going on. Janeway acts strangely distant, and retires to her quarters with a "headache." Chakotay visits Sickbay and calls for the Doctor, who beams in from elsewhere on the ship. Chakotay asks him to re-examine Janeway to see what the aliens may have done to her. Later, Chakotay gets a message from Supreme Archon Loth of the R'Kaal Imperium, warning that if Voyager does not surrender its warp core in ten hours, his armada will destroy the ship. Chakotay asks Seven of Nine and Harry Kim to pinpoint the source of that transmission. After finding out from the Doctor that the captain is normal, Chakotay confronts Janeway in her quarters about her decision. He makes up a story about Janeway's past that she pretends to remember, thus exposing her as an imposter. The imposter then overpowers Chakotay and knocks him out with a hypospray injection.
The imposter places the unconscious Chakotay in the ship's morgue and keeps his combadge, then returns to Sickbay and uses the mobile emitter to restore his identity - the imposter is the Doctor. The Doctor has been hearing the voices of two "Overlooker" aliens - the species that learned how to tap into the Doctor's perceptual subroutines over a year ago - and forced to do their bidding because they are holding the real Janeway hostage on their ship. On top of procuring the warp core, Zet, the leader, orders the Doctor to also acquire a series of gel packs. When Tuvok summons Chakotay, the Doctor downloads the commander's holographic template and takes on his identity. Tuvok informs him that the Flyer's com system is not damaged as the captain had reported. Meanwhile Janeway, being held behind a forcefield by the Overlookers, tries to bluff her captors into thinking the Doctor is fooling them, but Zet refuses to abandon his plan because the warp core is worth too much money.
On Voyager, the Doctor, using Janeway's voice, summons B'Elanna Torres to the captain's quarters so he can draw her out of Engineering in order to impersonate her there. While loading up gel packs in a case, the Doctor is approached by Tom Paris, Torres' husband, for a romantic interlude. After that awkward encounter, the Doctor goes to Astrometrics as Chakotay where Seven and Kim reveal that the R'Kaal transmission originated from inside Voyager, specifically Holodeck 2. The disguised Doctor goes there with Kim, who uses residual photonic displacement to find out who was last there. He realizes the R'Kaal was actually a hologram, and the underlying template was that of the Doctor's. Exposed, the Doctor injects Kim with a hypospray, and hides him also in the morgue.
Back in Sickbay, the Doctor talks to the Overlookers while listening to "The Blue Danube" waltz. Tuvok arrives and reveals that he's learned the Doctor downloaded the captain's holographic template while on the Flyer. When the Doctor tries to inject him with a hypospray, Tuvok is ready for the attack. The Doctor leaps through solid objects and grabs his mobile emitter to escape from Sickbay. Tuvok pursues him to a holodeck, where he's faced with a roomful of holographic copies of the Doctor. While Tuvok tries to disable the decoys, the Doctor takes a Jeffries Tube to Engineering and becomes Chakotay again, ordering an evacuation due to an imminent core breach. Paris informs Torres that he's detected the Doctor's emitter in her section, so the Doctor traps Torres behind a forcefield, activates his Emergency Command Hologram protocols and uses his command codes to eject the warp core. The Doctor then makes his way to the Delta Flyer and, using its modified tractor beam, tows the core away at warp speed.
Meanwhile Janeway helps the second Overlooker, Nar, repair a salvaged component, realizing she may be able to take advantage of his friendliness. Zet puts a stop to their interaction, just as the Doctor arrives in the Delta Flyer with the warp core. Zet says he will release the captain in exchange for the core, but instead he beams the Doctor over to their ship and imprisons him with Janeway. Janeway chews out the Doctor for not following her orders to refuse cooperation, but he insists he wouldn't let her be killed.
Back on the stranded Voyager, the crew finds Chakotay and Kim in the morgue and revives them. As they try to figure out how to track down the Flyer, the ship's com system starts playing "The Blue Danube" and won't stop. But the music contains several incorrect notes, so the crew realizes it was altered intentionally. Seven analyzes the harmonics and finds a pattern that appears to be a warp signature. She scans for that signature and finds it 6.7 light-years away. Since Voyager doesn't have warp, Tuvok and Paris take a shuttle to that location.
The Overlookers, meanwhile, decide to use the Doctor to infiltrate their Hierarchy's Surveillance Complex to steal valuable information, and start uploading new data and holographic templates into his matrix. When the Doctor takes on the form of an Overlooker, he starts to destabilize and has a hard time staying in one form. At that point Tuvok and Paris arrive in the shuttle to take back the Delta Flyer, and they get into a phaser fight with the Overlookers. Zet decides to jettison Voyager's warp core and detonate it, and Nar realizes that would kill the people in the other ships. Janeway and the Doctor escape from behind the forcefield and, while the Doctor struggles with Zet, Janeway works the controls to transport the warp core back out into space, allowing Paris to reclaim it with the Flyer. Zet asks Nar to help him overpower the hologram, but Nar chooses to knock out Zet instead, putting an end to the struggle.
In danger of permanently decompiling because of the excess subroutines, the Doctor is rushed back to Voyager where Torres and Seven try to stabilize his matrix. Certain he won't survive, the Doctor starts making several "deathbed confessions" to the crew, include the revelation that he's in love with Seven. But then Torres succeeds in saving his program, ensuring a long life for the highly embarrassed Doctor.
It is the 10th anniversary of the U.S.S. Voyager's triumphant return to Earth after 23 years in the Delta Quadrant. Kathryn Janeway is an admiral, Harry Kim is a starship captain, Tom Paris is a full-time holonovelist, and the Doctor is married to a human woman and has named himself "Joe." At a reunion party, Admiral Janeway talks with B'Elanna Torres, who is now Federation Liaison to the Klingon High Council, about arranging a political favor for a Klingon named Korath. Later, the admiral serves as guest lecturer in Commander Reginald Barclay's Starfleet Academy class about the Borg, but when a cadet asks a question about Seven of Nine, Janeway evades the subject. She's pulled away from class to receive a message from Ensign Miral Paris, the daughter of Torres and Paris, who is on a secret mission to arrange some sort of exchange between the admiral and Korath.
Admiral Janeway stops to say goodbye to Tuvok at his hospital room where he is suffering a neurological disorder that has destroyed his mind, telling him she may never come back. She then has the Doctor over to her apartment and asks him to procure for her a supply of Chronexaline, an experimental drug that can protect biomatter from tachyon radiation, for "classified" reasons. She arranges to get some downloaded information and a shuttle from Commander Barclay, and finally she visits Chakotay's gravesite, promising that when she's through things will be better for everyone.
Twenty-six years earlier, when Voyager is still in the Delta Quadrant, the pregnant Torres is having repeated occurrences of false labor, and Seven of Nine is developing a serious romance with Chakotay. Tuvok is concerned when he is defeated by Icheb in Kal-toh, so he visits the Doctor and learns his neurological condition is slowly deteriorating. Seven is playing Kadis-Kot with Neelix by remote when she is interrupted by the detection of high neutrino emissions indicative of a wormhole. Seven later tells the crew that the center of a nearby nebula may contain hundreds of wormholes, any of which could lead to the Alpha Quadrant.
Back in the future, the Doctor visits Tuvok, who has become increasingly agitated about the "disappearance" of Admiral Janeway, and blurts out that she's never coming back. Curious, the Doctor visits Commander Barclay to get in touch with Janeway, and Barclay says simply that she's out of town. But when Barclay starts stammering, which he hasn't done in years, the Doctor knows he's hiding something. Meanwhile Admiral Janeway has taken the shuttle to a moon where she meets up with Miral Paris, who introduces her to the House of Koroth. After dismissing the Ensign, Janeway meets with Korath, who has something for her but demands information on her shuttle's shield modifications. The admiral won't go beyond the original terms of their agreement, so she is shown out.
In the present time, Voyager enters the murky nebula and barely misses colliding with a Borg Cube. Captain Janeway orders the ship out of the nebula, refusing to go back despite Ensign Kim's appeal to not give up on those wormholes. Later, Seven asks the Doctor to perform a procedure he devised to remove a failsafe device in her cortical node, so she can pursue more intimate relationships -- specifically, with Chakotay.
Admiral Janeway tells Korath she's "reconsidered" his offer -- she'll give him the shield emitter, but first she has to inspect the device he's offering. Korath allows her to scan the device, whereupon Janeway attaches a transport enhancer to the device and beams it and herself to the shuttle. The enraged Klingons send one of their futuristic ships to fire upon her, but Janeway deploys a new armor technology around the shuttle that absorbs the phaser blasts. She jumps to warp and escapes, but when she arrives at her destination, she is met with the Federation starship Rhode Island, commanded by Captain Kim, who orders her to stand down. Kim has learned of her plan from the Doctor, who coaxed it out of Barclay, but Janeway insists the consequences are too great if she doesn't follow through, and asks him to trust her judgment one last time. Kim helps her prepare Korath's device -- a chrono-deflector which is now affixed on top of the shuttle -- and realizes it will burn itself out with one use. Janeway already assumed this would be a one-way trip. Unable to talk her out of the scheme, Kim beams back to his ship, and Janeway activates the chrono-deflector. Two Klingon ships decloak and begin firing, and Janeway is unable to deploy the ablative armor. The Rhode Island comes back and distracts the Klingons while Janeway activates a tachyon pulse.
Meanwhile on the present-day Voyager, Seven of Nine and Chakotay are having their first kiss when they are summoned to the Bridge. Some sort of temporal rift is forming in front of the ship, and Klingon weapons fire is being detected. But then a Federation vessel comes through the rift and hails Voyager. Captain Janeway sees the older version of herself on the viewscreen, ordering her to emit an anti-tachyon pulse from the deflector to close the rift before the Klingons come through. Startled, the Captain hesitantly fulfills that order and seals the rift, then asks what the hell is going on. Admiral Janeway says she's come to bring Voyager home. What she doesn't realize is that the Borg Queen is monitoring her transmission.
Admiral Janeway beams aboard Voyager and meets her younger self, and is moved to see a healthy Tuvok and Chakotay again. In Janeway's Ready Room, the Admiral reveals to the Captain that Voyager did eventually make it back to Earth after another 16 years, and the ship became a museum on the grounds of the Presidio. But the Admiral came to tell Captain Janeway to take Voyager back to the nebula as a shortcut home, using technology she brought to get past the Borg. The Captain wonders why she would want to tamper with the time-line, but the Admiral asks for her trust. In Sickbay, the Doctor confirms that the Admiral is genetically identical to the Captain, but 26 years older. He has also detected an implant in her brain, which the Admiral reveals the Doctor himself invented in the future to allow her to pilot a vessel with a neural interface. Seven of Nine enters -- to an emotional greeting from the Admiral -- reporting that the armor and weapons technology on the shuttle can be adapted for Voyager, and the Captain orders it done.
The crew busily upgrades the ship with the futuristic technology, and feels optimistic they might actually make it home this time. When Seven takes a break to regenerate, she is visited in her mind by the Borg Queen, who warns her not to let Voyager return to the nebula or it will be destroyed. Seven wakes up violently in her sparking alcove, and upon being cared for by the Doctor, reports the Queen's warning to the two Janeways. The Admiral insists the Borg are 30 years behind compared to the technology and tactics she's brought, so the Captain maintains course for the nebula.
When Voyager approaches the murky nebula, Captain Janeway orders the armor deployed, and the ship's hull is completely covered. Three Borg Cubes engage the starship, but their weapons fire is repelled. They scan the ship, then focus their fire on a specific section of the armor which weakens it. Voyager responds with the launch of transphasic torpedoes, which completely obliterate the Cubes with one or two shots each. Voyager then finds the center of the nebula, where the crew sees a massive Borg structure. Admiral Janeway orders Paris to enter an aperture in the structure, but Captain Janeway belays that order until she gets an explanation. Seven of Nine reveals the structure is a transwarp hub, one of only six in the galaxy. Angered that the Admiral didn't tell her about this, she orders the ship out of the nebula.
The crew learns the hub connects thousands of transwarp conduits to endpoints in every quadrant of the galaxy, perhaps the most significant tactical advantage the Borg have. Captain Janeway wants to know how to destroy it. But Admiral Janeway strongly objects to any such attempt, and insists on taking the ship home before the Collective can counteract the armor and weapons. The Captain pulls the Admiral aside and wonders how she got so cynical, arguing that they have a chance to save millions of lives. The Admiral reminds her of the decision that got her ship stranded in the first place, putting the lives of strangers ahead of her own crew. The Captain is willing to make the same kind of decision, but then the Admiral tells her that Seven of Nine is going to die. And her husband, Chakotay, will never be the same, and neither will Janeway. Along with 22 other casualties, Tuvok will succumb to a degenerative neurological condition that he hasn't told her about. She can prevent all that and get home today safe and sound.
Captain Janeway approaches Tuvok about his condition, and learns he can only be cured by mind-melding with members of his own family. But she also learns that Tuvok would rather destroy the hub than save himself. Even Seven of Nine refuses to listen to the Admiral's argument. In fact, the entire crew agrees that they'll allow their journey to take longer if they can accomplish something they believe in. The Admiral had forgotten how much the crew loved being together, and admits she was wrong to talk the Captain out of something she had set her mind to. But then the Captain proposes that there might be a way to "have their cake and eat it too."
The Admiral boards the shuttle, and the Captain injects her with a hypospray. The Admiral takes the shuttle through one of the hub's apertures and enters the Unicomplex where the Borg Queen resides. Using her neural interface, she enters the mind of the Borg Queen and tries to make a deal with her, in order to save the Voyager crew from themselves. She wants to Queen to send a Cube to tractor Voyager back to the Alpha Quadrant, in exchange for telling her how to adapt to the transphasic torpedoes. But the Queen detects the Admiral's shuttle, beams her over and injects her with assimilation tubules. Meanwhile Voyager deploys its armor and enters one of the transwarp hub's apertures. While the Admiral is being assimilated, the Queen orders vessels to intercept Voyager. But she realizes she no longer has control over the Collective. She realizes that when Admiral Janeway was assimilated, she released a neurolytic pathogen into the Collective, designed to bring "chaos to order." While in a transwarp corridor, Voyager launches its transphasic weapons and begins to collapse the transwarp hub. The Borg Queen, meanwhile, begins to literally lose parts of her own body as her Unicomplex begins to crumble in an array of explosions.
In the Alpha Quadrant, Admiral Paris and the present-day Barclay detect a transwarp aperture opening up less than a light-year from Earth, and every ship in range is ordered to converge there. In the collapsing transwarp corridor, a Borg Sphere bears down on Voyager as its armor begins to fail. Captain Janeway orders Lt. Paris to adjust course. The Borg Sphere emerges into the Alpha Quadrant and Starfleet vessels begin firing upon it. But then it explodes in a spectacular fireball, and Voyager emerges from within the debris intact. Admiral Paris welcomes Janeway back home, and promises him a full report. Meanwhile, a baby is being born in Sickbay -- Tom and B'Elanna's daughter. Paris is dismissed from his duties so that he can meet his new child and Captain Janeway orders Chakotay to take the helm and set a course for home. The Starfleet armada then escorts the long-lost Voyager back to Earth.
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