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The ship remains on Red Alert after Janeway, in exchange for safe passage through space, reaches an agreement with the Borg Collective to help them fight Species 8472, a race more malevolent than their own.
Although Chakotay strongly objects to the unpredictable collaboration, Janeway and Tuvok transport, with great caution, to the Borg Cube. When a drone attempts to temporarily assimilate Janeway by connecting a neuro-transreceiver to her, the alarmed Captain convinces them to instead choose a representative to communicate verbally with her. Soon, a vaguely human Borg emerges to speak for the Collective; designated Seven of Nine, she helps them prepare to engage the enemy - but when she boards Voyager, the entire crew is on edge. Meanwhile, the Doctor determines that the mysterious alien species is accessing Kes' memory.
Kes knows it's time to leave the U.S.S. Voyager when her body goes into a state of cellular flux and she experiences uncontrollable psychokinetic abilities which endanger the ship. Meanwhile, Seven of Nine's human physiology begins to reassert itself and threaten her life. When Janeway instructs The Doctor to completely remove her Borg technology, a fierce yet alluring young female begins to emerge.
As Lieutenant Torres reluctantly faces the Day of Honor, an ancient Klingon ritual which requires examination of one's behavior, the U.S.S. Voyager is forced to eject the warp core, and she and Paris must launch a shuttle to tractor it back. Soon, the U.S.S. Voyager is ambushed by the Caatati, a race almost completely assimilated by the Borg, who demand Seven of Nine as ransom. When the Caatati attack the shuttlecraft, Torres and Paris are left suspended in space and prepare to die, prompting Torres to confide to her crewmate that she loves him.
Chakotey is marooned on an unknown planet where the two inhabiting alien life forms are attempting planet-wide genocide against each other. Chakotay is captured by one of the tribes and comes to sympathize with them and their battle for survival against a ferocious enemy.
Aboard the U.S.S. Voyager, Harry Kim is assigned to work with Seven of Nine on the new Astrometric lab. Kim is uneasy working with the Borg, but their detail provides them with the basis of a friendship. However, Kim is rattled when Seven of Nine interprets his pleasantries as romantic seduction and she decides to further explore her resurgent humanity.
Seven of Nine escapes from the U.S.S. Voyager when she believes she is being summoned by The Borg. She arrives at the remains of a destroyed ship that she discovers to be the same vessel from which, as a young girl, she was captured by The Borg.
The crew begins to exhibit strange medical symptoms and the Borg, Seven of Nine, soon discovers the cause.
Distressed at the loss of his family and an entire colony of his people by a hostile alien enemy, Krenim leader, Annorax, has mastered time manipulation and can obliterate history, making entire lifeforms and civilizations cease to have ever existed. In this way, he hopes to restore his loved ones by erasing the enemy that caused their deaths. His well-calculated plans are thwarted by the incursion of the U.S.S. Voyager. Captain Janeway and her crew come between Annorax and his plans, for which it seems he will make good on his promise to destroy the starship.
A crippled U.S.S. Voyager, structurally weakened and shattered beyond operation, hides from the pursuing Krenim weapon-ship.
Most of the crew has abandoned the U.S.S. Voyager, leaving only a skeletal staff and the determined Captain Janeway on-board. With whole segments of the proud starship missing, and life-support systems failing, Captain Janeway is adamant about defeating the Krenim or going down with her ship.
A visit to the homeworld of the Mari, a race of telepathic beings, gives the U.S.S. Voyager crew a chance for some much-deserved ``shore-leave''. However, these beings, who have forbidden violent thoughts as well as actions have B'Elanna Torres arrested for involuntarily thinking of an angry retaliation to an incident. Tuvok becomes involved in her case and makes a startling discovery about the Mari.
Small and nimble alien spacecraft attack the U.S.S. Voyager, using high energy transports to break through the ship's shields, scan its contents and pluck off valuable equipment. Janeway and Tuvok beam down to the pirates' homeworld in search of the ship's main computer. To their surprise, they find Janeway's holographic Leonardo da Vinci, who becomes an essential part of their plans to retrieve the goods and leads them to the pirate king, Tau.
Neelix is preparing a shipboard feast on the eve of Prixin, the Talaxian celebration of family, when he is asked by Chakotay to join him and Paris on a shuttle mission. Neelix is all too glad to help, but the assignment proves to be fatal for him. Upon the shuttle's return to the U.S.S. Voyager, Seven of Nine, citing Neelix's diverse functions within the crew, applies Borg technology to reactivate him. Alive and shaken by his death, Neelix questions his assumptions about life -- and the promised afterlife -- as the Prixin festivities commence.
The Voyager crew is attacked by a species who occupy a parallel reality in the human dreamstate. Only Chakotay, with his native knowledge of waking dreams, knows how to lead a counterattack,
In an attempt to communicate with Starfleet, The Doctor is transmitted thousands of light years to an experimental prototype Starfleet vessel overrun by Romulans.
Thanks to the success of the doctor's previous mission (``Message in a Bottle''), Voyager has at last made contact with Starfleet Command by using a far-flung array of alien relay modules to communicate with Earth and let them know that they are, indeed, alive - -although still many light years away.
Miraculously, the ship begins receiving messages, transmitted across the vast distances over the same relay system, from relieved family and friends back home. Voyager's crew is elated to finally hear from loved ones after so many years. However, for Captain Janeway and others, their joy is tempered by bittersweet news.
Many messages are still being held at the module. Voyager proceeds to the alien craft to attempt retrieval of the remaining transmissions. Tuvok and Seven of Nine are ordered to board a shuttle and inspect the craft. Before they can, however, they are captured, beamed aboard an alien vessel and trussed-up like animals as a rude introduction to the Hirogen, a hostile, alien race of hunters. Living for the thrill of the hunt, the Hirogens have targeted Voyager's crew as prey in their latest game.
Voyager encounters a Hirogen ship, adrift, with a critically wounded Hirogen hunter on board. Janeway orders that the alien be beamed into Voyager's sickbay, despite Seven of Nine's warnings that the formidable Hirogen would regard the crew as no more than prey to be hunted and killed. Janeway disavows her concern and brings the Hirogen onboard. His presence brings even greater danger when the creature that he has been hunting across space -- species 8247, lethal even to the Borg -- boards Voyager.
Janeway must now decide whether to let the Hirogen loose in the ship to subdue the other, more dangerous alien. Seven of Nine refuses to obey Janeway's orders, bringing the captain to invoke disciplinary action against her.
Kovin, an alien arms merchant, is on board the U.S.S. Voyager to barter his impressive array of weapons with Captain Janeway. As installation of the weapons will require a reconfiguration of the U.S.S. Voyager's schematics, Janeway orders Seven of Nine to assist Kovin. Seven complies, if only to get back into Janeway's good graces after their recent disagreements. However, an altercation between Seven and Kovin brings the Captain to believe Seven is once again non-cooperative - until The Doctor makes a discovery about Kovin and Seven.
Having invaded Voyager and discovered the many uses of the Holodeck, Hirogen hunters have been playing a deadly game with Voyager crew members, putting them through various scenarios in which they are being hunted down as prey. One of the scenarios takes place in occupied France, with the Hirogen as Nazi SS Officers chasing down Captain Janeway, Seven of Nine, Tuvok and Torres as members of the French Resistance.
Implanted with subdermal transmitters, the crewmembers have no knowledge that they have identities beyond the characters they are playing. Only the Doctor, forced to mend the steady stream of wounded crewmembers to sick bay, is conscious of the invaders. He soon figures out a way to disengage Janeway and Seven of Nine, who then must begin to figure out how to defeat the Hirogen at their own game.
U.S.S. Voyager comes to the aid of an alien, Steth, who claims to be the test pilot of a new spacecraft that has run into trouble. Paris, who has become weary of being on the U.S.S. Voyager, volunteers to help him repair his ship. However, Steth is able to copy Paris's DNA and swaps physical appearances with him. Paris is then left behind in Steth's ship while the imposter takes over his duties at the helm and leaves the real Paris behind. It isn't long before ``Steth'' is confronted by Daelen, another alien who is seeking her original form. Back on the U.S.S. Voyager, Janeway suspects something is wrong, but Steth assumes her appearance and takes command.
The crew is mystified when Captain Janeway begins an important, though highly secretive, operation in response to a strange subspace disturbance. Chakotay finally compels her to tell the crew so that they may help. Janeway explains that Voyager has detected a dangerous, unstable substance called the Omega. The molecule has the power to destroy space and Starfleet's highly classified operating order is to destroy the Omega whenever it is encountered. Seven of Nine speaks out to say that the Borg believe the Omega can be captured and neutralized for study, which puts her in conflict with Janeway's Starfleet mission.
Voyager encounters an alien vessel fleeing attack whose sole inhabitant is a female alien asking for Chakotay to help rescue her. The startled Chakotay leads an Away mission to the damaged ship to help the alien, Kellin, who claims that she and Chakotay met before. Back on board Voyager, Kellin claims to have been on the ship not very long ago and she fell in love with Chakotay. Now fleeing her home planet's repressive government, she seeks asylum aboard the starship. Chakotay, though drawn to her, doesn't know whether to believe her or not.
A curious holographic tableau is on display in a Kyrian Museum and the curator, Quarren, explains to visitors how the intervention of the Voyager spacecraft started an apocalyptic war on a planet inhabited by two species: the Kyrians and the Vaskans. Ethnic rivalries between the two races are still uneasy, seven hundred years after Voyager has come and gone, and some Vaskan visitors are appalled by the Kyrians reconstruction of history based on a few recovered artifacts. But more damaging information is on the way, when Quarren activates a newly discovered device containing active data. This turns out to be the holograph program for The Doctor, who soon finds himself on trial for war crimes attributed to Voyager and its crew over seven centuries ago.
With fuel dwindling to nothing, Voyager lands on a ``demon'' planet - so called because its environment is toxic to human life - to collect from its vast deuterium lode. Both Tom Paris and Harry Kim are suited up in protective gear and sent out to collect the precious deuterium, but return without their protective suits. Instead, it is now Voyager's environment that is poisonous to them.
Encountering a deadly radioactive nebula, Captain Janeway decides to save time by going through rather than around it and orders the crew into protective stasis chambers with Seven of Nine to take lonely command.
With the entire crew now in cryogenic sleep, and only the Doctor for company, Seven of Nine is the only living being walking the ship's hallways. The long and lonely journey through the nebula begins to play tricks on the former Borg's mind as she experiences what humans call ``hallucinations''. An alien, Trajis Lo-Tarik, also making his way through the nebula, asks to trade some vital supplies, but his presence unleashes a series of events that Seven can't decipher as to whether they are real threats - or even if Trajis himself is real.
The badly damaged encoded message received from Starfleet Command five months ago is finally translated by Arturis, an alien passenger recently invited onboard, whose species has a great affinity for language. The directive brings Voyager to a spacecraft, emitting a distinctive Starfleet warp signature, but totally unlike any Starfleet vessel known. With a propulsion system faster than warp speed, the ship is capable of bringing the Voyager crew to Earth -- crossing 60,000 light years -- within just three months. The crew is elated, but Captain Janeway expresses caution, even though they are all secretly hoping to be home very, very soon.
While the crew's excitement grows, so does Seven of Nine's anxiety about living among billions of humans. She asks Captain Janeway to let her depart Voyager and roam the Delta Quadrant on her own.
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