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When the Voyager crew finds an ancient artifact from Earth floating in space, their discovery leads them to an uncharted planet. After atmospheric disturbances force the crew to land Voyager on this mysterious planet, Captain Janeway leads an away team in search of the source of the SOS to be an old Earth aircraft. Upon further investigation, the team finds a massive chamber containing eight Earthings in cryogenic units, one of which is Amelia Earhart, the first woman aviator.
After releasing them from suspended animation, the Voyager crew comes under attack when a group of the planet's inhabitants mistake them for members of the Briori -- an alien race which abducted more than 300 people from Earth in 1937 and brought them to this planet as slaves. It's learned that over time, the slaves revolted and killed the aliens. The eight surviving "37's" became part of the planet's history and the cryogenic chamber was their shrine. Since then, the descendants of the original 300 cultivated the planet and created a home much like Earth.
The crew of Voyager is invited to stay, and Janeway must face her greatest challenge as she allows each crew member the personal choice to stay behind and begin a life among these kindred humans.
When First Officer Chakotay borrows a Shuttlecraft to perform the Pakra, a solitary Indian ritual commemorating his father's death, he inadvertently drifts into Kazon-Ogla territory and becomes the target of a Kazon youth attempting to earn his Ogla warrior name by killing the Federation enemy.
Striking back, Chakotay disarms and destroys the Kazon ship, but not before rescuing the young boy named Kar -- the only surviving lifeform -- by transporting him aboard the Shuttlecraft. Soon, the two are pulled via tractor beam aboard a larger Kazon vessel sent to investigate the explosion. Led by Razik and Haliz, the Kazon-Ogla hold Chakotay prisoner furing which her learns that because Jar has failed in his first mission, he doesn't earn his name and is sentenced to die... by Chakotay's hands.
Meanwhile, fearing their missing comrade is in danger, the Voyager crew -- with Kes and Neelix providing their expertise on Kazon -- sets out to find Chakotay.
The Doctor receives information that Voyager has suffered a massive Kazon attack and that most of the crew has abandoned ship, so he ventures from Sickbay, via remote holo-projection system, to aid those still on board.
Once he's on the ship's near deserted Bridge, The Doctor must determine what is and what is not reality. Much to his confusion and counter to his program, The Doctor shows human life signs when, during a struggle with a Kazon warrior, he experiences injury and pain. He meets Lieutenant Barclay, learns of Dr. Lewis Zimmerman, the holo-engineer who wrote his medical holographic program and amazingly, discovers that The Doctor has a wife - Kes. He's in a state of disbelief when Barclay tells him he must completely destroy Voyager.
Aggressive space-dwelling lifeforms attach themselves to the Starship, creating an electrophoretic field. The occurence increases Kes' metabolic activity and accelerates her reproductive process, causing her to prematurely enter the elogium -- the time of life when Ocampa bodies become fertile. However, the elogium occurs only once, so if Kes is ever going to have a child, it must be immediately.
Before making his decision whether or not he will father Kes' child, a bewildered Neelix seeks the advice of Tuvok. Meanwhile, while considering how long it may take to get the ship home, Janeway wonders if it may be necessary for the crew to start having children to provide the next generation of personnel.
Ensign Harry Kim is confused when he awakens to find himself on Earth -- in 24th century San Francisco -- working as a design specialist at Starfleet Engineering and engaged to be married to Libby. When he accesses his service records, they mysteriously indicate that he was never a crew member aboard the USS Voyager.
Although he has longed to be with Libby, his sense of duty compels him to return to the reality he knows -- and the Delta quadrant. Soon the dazed Kim meets Cosimo, an alien in the guise of a local shop owner, who explains that a temporal anomaly in the space-time continuum has transported him to an altered reality. Kim learns that if he recreates the circumstances that brought him to Earth and then flied into the time-stream, there's a chance he might be able to transport back to his reality. Upon further investigation, Kim finds information on his onetime crew member Tom Paris which indicates that Paris is a convicted traitor and alleged Maquis sympathizer. Kim travels to Marseille, France, to track down the recently paroled, drunk and disheveled Paris who claims he never made it aboard Voyager. Before long, Starfleet personnel believes Kim is a Maquis spy and puts him under house arrest.
A spatial distortion phenomenon occurs not only in space but inside the ship as well, changing Voyager's structural layout and completely disabling it. As Voyager is compressed and twisted by this unknown anomaly, the crew must work frantically to stop it.
Captain Janeway is incapacitated when she comes in contact with the strange force and soon, Neelix winds up missing. Meanwhile, the rest of the crew is trapped in a maze on Deck Six and the Doctor is confined to Sandrine's Bar as the force pushes inward, closing in on them.
When Kes spends free time with a smitten Tom Paris, Neelix is overcome with jealousy and instigates a messy fight with the Lieutenant. In the aftermath, the Captain sends the sparring pair on a shuttle mission to an M-Class planet to replenish food supplies. When their craft encounters an interference pattern, they crash on the planet. Seeking cover from trigemic vapors, Paris and Neelix seal themselves inside a cave and then discover they have company there -- an embryonic pod which hatches an alien baby, a repro-humanoid being. They must work together to sustain the newborn -- and preserve each other's life when its angry mother approaches.
As they ready for a first encounter with the Bothan alien species, a strange psionic field causes the Voyager crew to succumb to a delusional state and their most deeply buried thoughts to surface. During the catatonic crew member's ordeal, characters in Janeway's holonovel program become real and her beloved Mark appears; Paris faces off with his disparaging father, the Admiral; T'Pel and Torres is seduced by Chakotay. The ship is effectively disabled and it's up to an unaffected Kes and The Doctor to block the mysterious field.
While Chakotay leads an Away Team to drill for minerals on a moon's surface, they accidently disturb a village and encounter its defensive inhabitants - a group with Indian origins. A regretful Chakotay then experiences flashbacks of himself as a defiant 15-year-old who disappoints his father by not embracing the traditions of his tribe.
The natives employ a cloaking device to disable Voyager and the endangered Away Team must transport out, leaving Chakotay alone on the planet. When he's confronted by the aliens, they respond to his familiat tattoo marking. Chakotay recognizes the tones of their language as those of his own people and applies what he recalls from his father's teachings on their heritage to assure the natives of Starfleet's peaceful intentions and his sympathetic perspective. Along the way, he reconciles the conflicts he had with his now deceased father.
Meanwhile, while tending to the pregnant Ensign Wildman, The Doctor is challenged by Kes to show more compassion for his patients. So, he programs himself with a simulated flu virus to experience the disconforts living beings can feel.
The crew is hailed by Ocampa colonists on an alien space station who, at long last, lead them to the female mate of The Caretaker, a mysterious being who may have the ability to send them home. As Tuvok tutors Kes in honing her rapidly maturing mental abilities, it's concluded that her burgeoning powers have been extremely underestimated.
Tanis, a male Ocampa colonist, agrees to introduce Captain Janeway and her crew to an entity they call Suspiria, the female mate of The Caretaker. As the Voyager crew builds great hope of returning home soon, Tanis implores Kes to stay with her Ocampa people on the alien space station.
Kazon intruders board the U.S.S. Voyager and steal a Transporter control module. That collateral enables their leader, Culluh, to persuade rival sects to join together to conquer the Federation ship. Surprisingly, the mastermind behind the Kazon's scheme is an advisor with Cardassian, Marquis and Starfleet tactical experience - none other than Seska, the despised traitor and former intimate of Chakotay.
When Chakotay learns that Seska devised the Kazon plot, he secretly sets out alone - against protocol - to thwart her. The Kazon are one step ahead of him and he's quickly captured and brutally interrogated. With their First Officer in the hands of the enemy, the Voyager crew braces for a dramatic showdown, but Seska has more than one trick up her sleeve.
In search of precious tellerium needed to power the ship, Janeway, Tuvok, Torres and Neelix transport to an Alsaurian city occupied by the hostile Mokra. Tipped off to the Voyager crew's presence, Mokra soldiers capture Tuvok and Torres. During the commotion, Janeway is secreted away by Caylem, a local eccentric who believes she is his long lost daughter.
Neelix is not discovered and transports back to the ship with the necessary mineral and the bad news that the others have been discovered and taken prisoner. As Voyager searches for its arrested crew, Janeway goes undercover, forced to rely on her own devices and the help of her odd new protector, Caylem, to break into the prison and rescue Tuvok and Torres.
When the crew finds a deactivated humanoid robot with an unfamiliar power source floating in space, Chief Engineer B'Elanna Torres is able to repair this mysterious mechanical "man". When it comes to life, the sentient artificial lifeform, Automated Unit 3947, explains that its kind is near extinction and asks Torres to build a prototype for construction of more units. In accordance with the Prime Directive, Torres must decline the request, but when 3947's Pralor homeship is located, the robot abducts her and threatens to destroy Voyager unless she constructs the prototype.
Torres discovers that the robots are programmed to achieve victory while Janeway and her crew, taking measures to rescue her, find themselves in a war of alien robots.
After Voyager is severly attacked by Kazon and one of its crewmen killed, Chakotay appeals to Janeway to start thinking more like the Maquis. Janeway knows she must strengthen Voyager's position in the quadrant and, although it's a difficult decision and is against her beliefs and training, she agrees to take steps toward a strategic alliance with leaders of several Kazon factions. When they come together for a conference, it's eminently clear that there are no rules in this region of space.
Seeking an intermediary to begin talks with the Kazon, Neelix shuttles to Sobras, a planet with a Kazon settlement. There, he makes contact with an acquaintance, Jal Tersa of the Kazon-Pommar. Meanwhile, Janeway's initial meeting with Culluh and Seska is unsuccessful but Neelix is able to befriend Mabus, a governor of the Trabe, an exiled sect and bitter enemies of the Kazon. Thinking that the Trabe have compabible goals of peaceful co-existence, Janeway forms an alliance with them - with deadly results.
Lieutenant Paris makes history by becoming the first person to make a transwarp flight. But, soon after his shuttle returns from Warp Ten, he undergoes startling biochemistry changes. His cell membranes begin to degrade and, despite The Doctor's best efforts, Paris dies. Hours after the pronouncement of death, Paris is discovered breathing, his body going through accelerated mutations which leave him radically transformed into a bizarre and terrifying cross between a human and amphibian.
When a crew member is murdered, Tuvok's investigation leads to another crewman, Ensin Suder, who finally admits he is the perpetrator. Vulcan instincts prohibit Tuvok from determining a logical motive for committing such a crime, so he attempts to understand the violent impulses of a criminal by performing a mind-meld on Suder - with deadly results.
When Tuvok removes himself from duty, The Doctor must initiate treatment which removes Tuvok's emotional suppression abilities. Meanwhile, Chakotay puts Paris on report for running an illegal gambling operation and Neelix embraces his role as the ship's Morale Officer.
Voyager spots a Cardassian designed, self-guided missile carrying a warhead capable of significant destructive force. As it travels towards Rakosan, a heavily populated planet, Torres reports that she's partly responsible for its virtually unstoppable status. When she was a Maquis, she intercepted it and changed its program to assault the Cardassians, but it later went astray and now she's the only hope in stopping it. So, Torres volunteers to transport to the missile's interior and reporgram it again. But, before she can detonate the warhead, the onboard computer tries to destroy her first. Meanwhile, Jonas transmits the classified information on the mission to Seska.
A rebel Q (Gerrit Graham) escapes imprisonment from inside a comet and demands asylum aboard the U.S.S. Voyager. Just as quickly, the well-known Q arrives to force the escaped Q backto the Continuum, the extradimensional domain in which their immortal kind exist. Meanwhile, the escaped Q proclaims that if Captain Janeway grants him sanctuary, he intends to commit suicide to end the tedium he has endured as an immortal being.
Noting the dictates of Starfleet protocol, Janeway holds a hearing to consider the request for asylum. The tables are turned on Q as Federation personal preside over a trial in which he must defend the Q Continuum and the ever-logical Tuvok acts as counsel for the escaped Q. A courtroom drama ensues when Q calls himself to the witness stand along with a varied group of other people including Commander Riker, whose lives were profoundly changed by Q's influence.
Voyager detects a distress call from a weakened lifeform aboard a small spacecraft and quickly beams a deathly ill Viidian female to Sickbay. The Doctor starts treating her for advanced stages of the Phage by transferring her decaying body into stasis and creating a temporary, healthy holographic program of her being. As he becomes acwuanted with the alien, a hematologist named Danara Pel, something momentous occurs - his adaptive program allows him to experiance love and romance.
Lieutenant Paris continues to be insubordinate and espionage is more complicated than Jonas thought when Seska instructs him to plan an accident which will damage Voyager's warp coils.
Neelix, a suddenly self-proclaimed journalist, haers a rumor that a fellow crew member has expressed displeasure with Starfleet and requested leave. Soon, Tom Paris is relieved of duty to become a pilot with a Taalaxian convoy - leaving a saddened Voyager crew behind. Almost immediately, the Kazon-Nistim and the scheming Seska attack the Taalaxian fleet, kidnap Paris and attempt to coerce classified information from him. Meanwhile, Neelix suspects someone aboard Voyager has been secretly communicating with the Kazon and his sleuthing leads him directly to Paris.
Astounding consequences occur when Voyager, while attempting to evade pursuing Viidian vessels, enters a plasma cloud. Before they can clear it, the engines stall, anti-matter supplies drain and Proton bursts, originating from within the ship, cause heavy casualties and breach the structural integrity of the hull. When Ensign Kim and Kes disappear into a void in space, Captain Janeway discovers a duplicate Voyager with an identical crew exists in a parallel universe.
While the crew feverishly attempts to contain the worst onboard disaster ever, The Doctor struggles to keep alive Ensign Wildman's newborn, half-human, half-Ktarian baby. Then Janeway discovers that although a divergence field has caused all sensor readings to double and every particle on the ship to duplicate, there is not enough antimatter to sustain both vessels. As the Viidians close-in on them, she meets the other Janeway face-to-face to determine a solution, knowing only one of the two ships can survive.
Tuvok and Bennet's shuttle crash lands on a sacred haven for the Drayan, an alien race which has shunned outside contact for decades. While Bennet lies dying from his injuries, three frightened Drayan children venture out from hiding. The young ones tell Tuvok that they have been abandoned by their people to die on the planet, and beg his help in saving them from imminent arrival of the "morrok" - the messenger of death.
While Tuvok tries to calm the tiny trio, he cannot comprehend why a society would forsake its children. Then, during the night, two of the youngsters mysteriously disappear. Meanwhile, Janeway makes contact with the Drayan's First Prelate, Alicia, and in the course of trying to rescue Tuvok and the remaining child, there is an amazing revelation about this mysterious race.
Voyager activates an automated messages from members of the Kohl settlement who, years earlier, survived an environmental catastrophe by submitting themselves into artificial hibernation. When the crew transports the Kohl's hibernation pods on board, they find humanoids in deep stasis with supressed metabolic activity - but with active minds and complex sensory systems controlled by a computer - and that is where the nightmare begins.
In an effort to help the Kohl people, Torres and Kim equip two pods with Starfleet technology and submit themselves into stasis. With their mental and physical activities closely monitored, they enter the environment created by the computer attached to the Kohl pods. Once there, Torres and Kim find that the humanoid's dreadful fears about recovery and survival have caused their computer program to manifest a devious, omnipotent clown - the idealization of their fear - and a cast of other nightmarish characters. Then, the clown holds Torres and Kim hostage while making increasingly unreasonable demands of Janeway.
A bizarre occurrence causes Neelix and Tuvok, who are attempting to transport back to Voyager from an away mission, to arrive aboard ship as one. The crew is astonished when a strange but oddly familiar alien humanoid with dark speckled skin and pointy ears - which is neither Tuvok or Neelix - appears. The Doctor's bio-scanner shows that the Neelix and Tuvok's patterns have merged, causing the pair to become one entity - Tuvix - a humor-filled, logic defying fusion of the two crewmen.
While Tuvix assimilates and starts to become a valued member of the team, Kes struggles with the fact Neelix may not be part of her life anymore. Meanwhile, The Doctor devises a method to restore Tuvok and Neelix, except for one variable - Tuvix doesn't want to die. When The Doctor, who is programmed to follow certain ethical guidelines, cannot perform the the separation, Janeway is left with a monumental decision.
When Janeway and Chakotay contact a deadly virus from an insect bite, the Doctor cannot find a cure. Unable to perform her duties, Janeway is forced to turn over permanent command of the ship to Tuvok and retreat, with Chakotay, to a small planet which shields the effects of the fatal disease.
As Voyager moves out of her communication range, Captain Janeway leaves Tuvok with strict orders not to contact the Vidiians for help even though they may have more sophisticated medical technology to handle the crisis. While the ship's crew is struck with the harsh reality of abandoning their leader and first officer forever, the former Captain and Commander, alone on a strange planet, awkwardly drop protocol and begin to explore another side of their relationship.
In an emergency message to Chakotay, Seska discloses that their newborn son has been banished by Culluh to a servant colony. Chakotay feels conflicted about rescuing the baby because he was manipulated into fatherhood by Seska. When the crew detects a distress signal from a Kazon shuttle, they transport aboard the critically injured Teirna, a former aide to Seska, who delivers the news that Culluh has killed Seska. So with Teirna restricted to secured quarters, Voyager heads on a rescue mission through the Kazon-Nistrim territory where Kazon raiders viciously attack the ship. Before long, the fierce battle is over and the Voyager crew has lost - outwitted by their most bitter foe. Surrounded and defenseless, Captain Janeway must give up the ship to the Kazon.
The crew must accept that they've been tricked by Culluh who relishes the help of Voyager. At his side is an alive and well Seska who taunts Chakotay with their son. Then, the Kazon abandon the 148 members Voyager crew on the surface of Hanon Four, a primitive, ferocious planet. Stripped of their technology, they must use the most basic skills to survive. While they watch helplessly, their enemy lifts off the surface with their ship but, unbeknownst to the Kazon, two Starfleet crew members are stowed away on board.
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