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In the sixth-season opener, the Voyager is attacked by the aliens, and as Janeway plots to recapture Ransom and his crew, the Equinox is equally determined to escape with the Doctor and Seven of Nine as hostages.
A visit to a space station brings Seven of Nine into contact with her former Borg crewmates, Two, Three and Four of Nine, who wish to access her memories in order to recall their break from the collective.
Torres confronts a dark side of her Klingon ancestry when she asks a skeptical Janeway to allow doctors to induce a coma-like experience that will allow her to aid her condemned mother who is held aboard a mythic Klingon death barge.
The Doctor's daydreams take on dangerous dimensions when an alien voyeur sees those fantasies as reality.
Paris's plans to refurbish a used shuttle create big trouble for Voyager when the shuttle's computer manipulates his mind to complete its own plans for repair. It imperils the entire crew.
Janeway and a Keset agent rush to uncover why a mysterious energy force is causing Tuvok's Vulcan physiology to endure severe neurological trauma in the form of mental distress and emotional unpredictability.
The Voyager runs afoul of hostiles when the ship becomes enmeshed in a subspace corridor, leading to an encounter with the vengeful survivors of a devastated world who plot to hijack the ship in order to retaliate against their ancient enemies.
The Voyager is nearly consumed by a massive rolling ball of energy but curiosity about the rare phenomenon prompts Janeway to launch a probe to investigate and search for a missing 300-year-old U.S. spacecraft trapped inside - a risky maneuver that may cost the lives of the shuttle crew.
As Voyager shadows the powerful anomaly known as the Graviton Ellipse, Seven of Nine reluctantly joins a fascinated Paris and Chakotay on the shuttle as they look for the legendary Ares Four, the command module from an early manned mission to Mars. However, once found, the attempt to retrieve the craft and its noble dead pilot proves treacherous, and the small crew must improvise if they are to return at all before the ellipse disappears again into lethal subspace.
When Voyager encounters an alien whose space "catapult" can speed them back home, a data-overloaded Seven of Nine causes chaos when she incites a civil war then divides the crew with secret allegations of treachery and insurrection.
While Janeway debates accepting the use of an alien's technology that can cut their trip back to the Alpha Quadrant by years, an earnest Seven of Nine processes accompanying information and convinces Chakotay that the captain is sabotaging the true mission of Voyager. Likewise, she privately informs Janeway of a budding rebellion, mysteriously fanning flames that threaten to tear the ship apart.
In San Francisco, an obsessed former Enterprise engineer Reginald Barclay recruits Counselor Deanna Troi to help him communicate with the distant Voyager via a radically innovative system that puts him at odds with his superiors.
Assigned to the Pathfinder Project, Barclay secretly creates a startlingly realistic simulated hologram of the Voyager and its lifelike crew which he believes has aided his quest to send a one-way message to the actual ship 60,000 light years away. However, his unorthodox manner and single-minded passion for the project anger his commanding officers, forcing Barclay to risk everything when he disobeys orders and tries to generate his transmission through a temporary micro-wormhole.
Captain Janeway and her crew enjoy some hard-earned leisure time in the holographic setting of a charming Irish village where she can't help falling for a ruggedly handsome townsman - but their holiday is darkened by an approching wave of deadly neutron radiation.
Created by Paris as a diversion for himself and his mates, sunny Fair Haven offers Janeway a deceptively realistic fantasy figure named Michael, whose physical and intellectual specifications are made to order for her. Soon, her attention is commanded by the trailing edge of a speedy wavefront that poses more of a threat than anyone knows.
When Voyager becomes ensnared in the orbit of a strange, primitive planet -- its energized core enables it to rapidly develop into a society with warp technology. So Janeway briefly transports The Doctor to the alien world, only to learn that the presence of Voyager has inspired invention among the society, which without warning, aims its own weapons at Voyager.
The Doctor's ego soars when Voyager engages an advanced but arrogant race which is entranced by the medical officer's passable singing talent, granting him instant rock-star status that tempts him to leave the ship for his legions of fans.
Janeway and the crew are perplexed by the effect that The Doctor's voice and variety of song selections have on such a superior alien culture as the Qomar. Millions of them mob his concerts, countless ``fan mail'' messages arrive and groupies abound, but one particular female Qomar catches the good Doctor's eye, and he ponders resigning his commission to stay behind.
Post-traumatic stress disorder is pervasive after Chakotay and his shuttle crew begin hallucinating -- convinced they participated in a massacre on an alien world.
Tuvok and Seven get captured by a character named Penk. Tuvok is pretty badly injured, and Seven is forced to fight in their "pit fighter" type of game called Tsunkatse to save Tuvok's life.
Chakotay, Kim, Paris and Neelix are taken hostage when the Delta Flyer is captured by a Borg Cube. The Borg will return the crewmembers in exchange for Voyager's navigational deflector. However, Voyager will be unable to go to warp without it. Seven of Nine tells Captain Janeway that the Borg most likely want Voyager's deflector in order to contact the Collective because their own is damaged.
While stalling the Borg, Janeway tells them that she is sending Seven over to make sure that her crewmembers are unharmed. Aboard the Borg Cube, Seven discovers that it is manned by neonatal Drones, or children. The children insist that the Borg will come for them once their link is re-established.
Because Voyager cannot give up its deflector, Janeway offers Seven's services in repairing the Cube's technology. One of the Borg children tells Janeway that she has exactly two hours before one of the hostages dies. While speaking with the Borg children, Seven tries to jostle their memories in hopes that they will turn away from the Collective and come aboard Voyager.
Problems begin to arise when Voyager runs a Holodeck program non-stop. Characters within the holographic re-creation of Fair Haven become suspicious of the Voyager crew when they begin to notice strange, otherworldly happenings.
The city of Fair Haven is set within 19th century Ireland. After several incidents in which Fair Haven residents observe Voyager crew members use 24th century technology, the townsfolk gather and exchange the similar stories. \npar As the townsfolk begin to recognize that their existance is not what it seems to be, the safety of anyone from Voyager visiting Fair Haven is at risk.
A transmission from a rogue alien ship reveals dead starship crew member to be alive, asking for immediate sanctuary aboard Voyager and an old friendship becomes a love affair while alien genes affect the future.
The oldest of the Borg children is reunited with his parents -- to Seven of Nine's dismay, since she has grown fond of him. As it turns out, the child is a living time bomb infected with the pathogen that killed the adult drones. Voyager must decide whether to interfere by returning for him.
Janeway shepherds three troubled crew members on a short mission away from Voyager to help them adjust to the demands of their jobs and recognize the constraints of their personalities. But an unexpected attack threatens their lives, demanding that all four work in full interaction and complete unity in order to survive.
A band of Delta Quadrant con-artists have stumbled across the greatest scam of their careers: impersonating Captain Janeway and her senior officers Chakotay and Tuvok. Using their new identities, they move from system to system engaging in a series of lucrative deceptions.
Eventually, the real Captain Janeway and her crew are blamed for these deceptions when the con artists do not deliver the goods as promised. Ultimately, the Voyager crew must either bring the imposters to justice, or pay for their crimes.
Torres becomes the obsession of a well-meaning alien poet who uses her Voyager stories as inspiration for his theatrical work.
Kes returns a vengeful woman bent on destroying Janeway and Voyager. Using her advanced mental abilities, Kes journeys into the past, intent on delivering the crew into the hands of one of their earliest and most dangerous enemies, the Vidiians who crave human body parts.
The Doctor transmits his program back to the Alpha Quadrant in order to save the life of his creator, Dr. Lewis Zimmerman, with the help of Reginald Barclay and Deanna Troi.
Neelix, in charge of pacifying the Borg children when lights on the ship flicker and fail, lets his imagination run wild and turns reality into a fantastic but utterly believable story which mesmerizes the children into believing that a ghost actually dwells on Deck Twelve.
As Neelix tells it, months ago an electromagnetic lifeform took possession of the ship, shutting down all life support systems, while trying to communicate with Janeway its need to return to the nebula from which it came. Area by area was cordoned off by an invisible force field, and injected with poisonous gas, while the captain set up an emergency command post in the Engineering Room.
An enclave of Borg drones create a virtual escape, a paradise of freedom and nature, which they enter mentally through their regeneration cycles, but which vanishes from memory when they awake. Janeway recognizes this mutation as a potential crevice through which Borg resistance may be encouraged - and with Seven of Nine embarks on an undercover entry into the Borg transponder to plant a target virus.
Story
When the Borg Queen discovers that some of the Drones have a recessive mutation that allows them to travel to a place where they become almost ``human'', she is determined to stop them.
Seven of Nine awakens from a ``nap'' in an uneasy state. She Dreamed of a beautiful forest with trees and flowers. In this place people knew her as Annika and she was almost human. Seven is not used to "dreaming" so she is unsettled by the experience.
Paris, thinking he is being reprimanded by the crew for being late, is surprised by being awarded an Officer's Pip. He is then reinstated to Lieutenant by Captain Janeway.
Seven retires again to her alcove wearing the cortical monitor the Doctor gave her and closes her eyes. She finds herself back in the beautiful forest. She tells herself that this is "not real" when suddenly a voice is heard assuring her that it is. It is the voice of Axum, someone she has seen before in this environment. He calls this place Unimatrix Zero.
Axum explains to Seven that Unimatrix Zero is a place where the Drones go during regeneration so they can exist as individuals. The Collective knows about this place but cannot find it. The Drones who visit Unimatrix Zero have the recessive mutation that the Borg Queen is trying to find and destroy.
Axum informs Seven that she used to visit Unimatrix Zero before she escaped the Collective. She too has the recessive mutation that only one in a million Drones has. Axum tells her that the Collective has found a way to detect them, so it is only a matter of time before they find enough of the Drones to isolate the interlink frequency and demolish Unimatrix Zero.
Axum begs Seven for her help, even though she is no longer a part of the Collective. Seven is their only hope because unlike her, after the Drones complete their regeneration they have no memory of Unimatrix Zero.
When Seven awakens she informs the crew of what she encountered. The Doctor confirms that she was not just having a dream, she never reached REM, therefore what she is telling the crew is real. Seven asks the Voyager crew for their help to save Unimatrix Zero.
Meanwhile, the Borg Queen is coming closer and closer to finding Unimatrix Zero. She has continued to dismantle other Drones in order to observe their parts and find a way into Unimatrix Zero.
Janeway feels that the crew should help, because it is a new aspect of the Collective and a potential weakness. They begin coming up with a plan to help the Drones.
Tuvok suggest a Vulcan technique known as the ``Bridging of Minds'', Janeway agrees. Janeway, Seven, and Tuvok will be hooked up to monitors. Tuvok will oversee their thoughts and Janeway will go with Seven back to Unimatrix Zero.
Upon their arrival they find Drones, sent by the Borg Queen, trying to destroy Unimatrix Zero. A battle ensues and Janeway defeats the last of the Drones. The Borg Queen has seen the fight through the eyes of a regenerating Drone and does not like what she sees. Janeway assures Axum that they will help defeat the infiltration of the Borg Queen's Drones into Unimatrix Zero.
Janeway and Seven begin working on a plan to help Axum and the others. The crew is trying to find a way to deploy a highly experimental ``nanovirus'' designed to target all the Drones with the recessive mutation and reprogram their memory centers. That way, when they leave their alcoves they will retain their memories. Janeway tells Seven to go back and reassure Axum that they are working on a plan and will be there as soon as they can.
Seven arrives at Unimatrix Zero and things have gotten worse, however the Klingons have banded together and are fighting off the Borg Queen's Drones. Axum confesses to Seven that they were involved before she escaped the Borg. They had promised not to leave one another, but as things got worse Axum insisted that she leave him behind and save herself. Although Seven feels familiar with Axum and Unimatrix Zero, she still does not remember what he is talking about.
Back on Voyager, Janeway is preparing to transform herself into a Drone in order to implement the nanovirus, Chakotay does not think it is a good idea. While they are arguing, the power beings to flicker and the command center becomes dark and foggy. The Borg Queen appears on the screen and threatens Janeway and her crew by informing them that she knows they have been in contact with Starfleet. The Queen informs Janeway that if she becomes involved with helping Unimatrix Zero, Voyager will have a difficult time making it home. Janeway does not back down, frustrated, the Borg Queen disappears and the crew knows they are going to have a fight on their hands.
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