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Seven of Nine is led to a place known as Unimatrix Zero; a place where Borg drones are individuals for a short period of time during their regeneration. However, once their regeneration is complete, all recollection of the event is erased. Captain Janeway uses this to form a plan of attack that would create a mutiny from within the Collective.
When Voyager shuts down main power and interrupts the regeneration cycle of the Borg children, Neelix keeps them entertained by telling the story of why a certain section of Deck 12 is off-limits, and how the space-dwelling creature that lives there came aboard and "haunted" the ship.
News reaches Voyager through the up-and-running Pathfinder project that the Doctor's creator, Lewis Zimmerman, is critically ill. In an attempt to save his life, the Doctor's program is transmitted to the Alpha Quadrant, but once there, he finds Zimmerman does not want to be examined by an "obsolete" EMH program.
An older Kes returns to Voyager to take revenge on Janeway for taking her away from her homeworld too young. Using her telekinetic powers to travel through time, Kes intends to deliver Voyager to the Vidiians and "rescue" her younger self.
A poet discovers an unconscious B'Elanna Torres in the damaged Delta Flyer, after it crash landed on his planet. In need of inspiration, this poet intends on using B'Elanna and the stories of Voyager in his plays, to win favour with his warlord patron.
A group of con artists impersonate Captain Janeway and the crew of Voyager. The crew must find the imposters soon, or they, themselves will be punished for the con artists' crimes.
When an efficiency report reveals that three of Voyager's crew members are failing to meet expectations and integrate into the rest of the crew, Janeway decides to take them on their first away mission. However, what awaits the Delta Flyer on that mission will present a formidable test for them all.
Seven becomes emotional when Icheb's parents are located, and it is assumed that he will leave Voyager to rejoin them. However, she later becomes increasingly concerned when it appears that they were not honest about the circumstances of his original assimilation.
A mysterious female alien contacts Voyager, claiming to be Ensign Lyndsay Ballard, who had been killed on an away mission years earlier.
The inhabitants of the holo-city of Fair Haven suspect the Voyager crew of having mystical powers when they witness the use of their futuristic technology.
Borg children who were rejected by the Borg as unworthy drones abduct Chakotay, Kim, Neelix and Paris.
While on shore leave, several crew members take in matches of a popular bloodsport called Tsunkatse. However, the vacation comes to an abrupt end when Seven and Tuvok are abducted, and Seven is forced to compete in the Tsunkatse to the death.
The crew of Voyager experience vivid memories and dreams of a battle they don't remember having, with an enemy they have never encountered.
When the Doctor's singing talents are discovered by a technologically superior race, his new found popularity makes him consider resigning his commission to stay on the alien world with his millions of adoring fans.
When Voyager is trapped in orbit of a unique planet, they learn that time moves far faster on that planet than in the rest of the galaxy. Although Voyager is stuck in orbit only for a matter of days, from the perspective of the planet, the "Skyship" has been watching them for centuries, and becomes a guiding force for the development of their civilization.
While the crew enjoys some relaxation in Tom Paris's latest holodeck program, an Irish village named Fair Haven, Captain Janeway falls for a holographic barkeep. However, problems soon arise for the crew, as a deadly neutrino wave approaches Voyager.
Back on Earth, Lieutenant Barclay becomes obsessed with finding a way to communicate with Voyager.
A data-overloaded Seven of Nine starts making accusations of conspiracy when Voyager encounters an alien with technology that can catapult the ship years closer to home.
Crew members are awestruck, and try to help Seven to appreciate the value of history, when a dangerous anomaly emerges from subspace, and the Voyager crew discovers it contains the remains of a 21st century manned Mars probe.
Under attack by the territorial Turei, Voyager sets down on an uninhabited planet to hide and make repairs. In a cavern under the surface, they discover and revive the final remaining survivors of the Vaadwaur, the planet's original civilization, who had been in stasis for nearly 900 years. As Voyager and their new allies prepare to engage the Turei, there is reason to fear that the Vaadwaur are more dangerous than originally suspected.
After being attacked and later revived, Tuvok develops new interests, displays emotion, and befriends Neelix.
Tom Paris persuades Chakotay to allow him to buy a shuttle from a junkyard. While repairing it, the ship begins to take control of Tom's mind.
The Doctor programs himself with the ability to daydream. When an alien spy gains access to The Doctor's visions he mistakes them for reality.
During a near-death experience, B'Elanna finds herself aboard the Klingon Death Barge, a spectral vessel which transports dishonored souls to Grethor. After seeing her mother there, B'Elanna risks her life to go back and save her mother's soul from this fate, even at the cost of her own.
While Voyager is docked at a space station, Seven of Nine is approached by three former Borg drones from her former unimatrix, who, despite being free from the Collective, are neurally linked to each other. Tracing the origin of this link to an accident eight years before, in which they and Seven were the only survivors, the three former drones believe Seven is the only one who can help them sever the link and achieve true individuality.
Janeway becomes obsessed with trying to capture Captain Ransom, no matter what the cost.