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The inevitable finally happens, as Voyager enters Borg space. However, they soon encounter a new threat, in a species even more powerful and dangerous than the Borg.
One by one, the crew of Voyager go missing and are replaced by strangers who claim they have no idea how they arrived. Soon, nearly the whole crew is gone, and there is no way of stopping the strangers from appearing and overrunning the ship.
An alien palaeontologist discovers a common ancestral link between his people and humans. He believes that this proves that his people, the Voth, evolved on Earth and migrated to the Delta Quadrant millions of years ago, but his government is not as willing to believe his interpretation of the evidence.
The Doctor decides he should create a holographic family in order to expand himself. When B'Elanna is disgusted by its unrealistic perfectionism, she alters the program to include random events and outcomes with interesting and devastating results.
Kes begins traveling backwards through time from the moment of her death. With each shift, she comes closer to a solution but she also grows months and years younger at a time.
Harry Kim experiences strong senses of deja vu in an unknown region of space. He soon learns that he is native to this region and that he is T'Karian, not human.
While on an away mission to help a planet being bombarded with asteroids, Neelix comes up with a dangerous plan to re-establish communication with Voyager. However, he is pushed to the limit when Tuvok's negative attitude toward him becomes too much to bear.
The Doctor tries to improve his programming by incorporating traits from famous and historical people, but is soon overwhelmed by the dark sides of their personalities.
Chakotay responds to a distress call, and discovers a group of different species, many of which originate from the Alpha Quadrant, living on a planet stricken by conflict. After Chakotay learns that they are all de-assimilated Borg, a group of colonists make a very unorthodox and dangerous request of Voyager.
Ensign Vorik expresses his desire to mate with B'Elanna during his Pon-Farr. After they get in a brawl over the matter, Torres begins showing signs of the Pon-Farr herself.
Captain Janeway repeatedly dies after she and Chakotay crash into a planet in what appears to be a time loop. Soon, her deceased father appears and tells her that she is dead and must accept her situation and move on.
Ensign Kim asks Tuvok to teach him Vulcan emotional control techniques when he falls in love with a holodeck character named Marayna. However, Kim soon becomes jealous when Marayna shows interest in Tuvok.
Voyager encounters a region of space named the Nekrit Expanse. Since Neelix has no knowledge about the space after this point, he tries to make himself useful to the crew by trying to obtain a map from an old friend named Wixiban, who in exchange, asks for Neelix's help with some less-than-reputable dealings.
Janeway and Neelix return from an away mission to find Voyager adrift in space and the crew barely alive. They soon learn that the ship has been overrun by viral life forms that are rapidly growing in
Voyager encounters several supernova in a small region of space. Q soon appears and reveals that they are the after-effects of a civil war within the Q-Continuum. He believes that the solution is for him to produce a child, and he has chosen Captain Janeway as his mate.
An injured alien named Tieran transfers his consciousness into Kes' mind moments before he dies. He then gains control over her and uses her abilities to steal a shuttlecraft and return to his home world to attempt a political coup.
Voyager must find a way to stop Starling, before his attempted use of the timeship destroys Earth's Solar System. Meanwhile, while trying to rescue Paris and Tuvok, Torres and Chakotay are captured by a militia cell who believe that they are from the government.
Both Voyager and a 29th century Federation Timeship, the Aeon, are pulled back in time to Earth in the late 20th century. The Aeon crashes in the Sierra Mountains during the 1960s, while Voyager appears in orbit around Earth during 1996.
Kes accidentally intrudes on a religious shrine and is almost killed by a strange energy beam. Told there is nothing that can medically be done to save her, Captain Janeway undergoes a spiritual quest to ask the "spirits" to spare Kes's life.
After Voyager encounters a telepathic species, B'Elanna starts having powerful dreams that depict the life of a woman and her lover in a time of great political and social upheaval.
Voyager discovers a pair of Ferengi, who arrived in the Delta Quadrant via the Barzan Wormhole, masquerading as gods to a primitive culture. The crew must find a way to put an end to this exploitation, while trying to use the same wormhole to get them home.
Voyager must find a way to cross a region of space owned by a mysterious race of hostile aliens without being detected. Meanwhile, Torres and Kes must work quickly to save The Doctor when a malfunction in his program causes him to lose his memory.
Paris and Kim are sent to an Akritian prison after being accused of a terrorist bombing, where they are thrown in among hardened killers. When the crew of Voyager finds out that Paris and Kim have already been tried, convicted and sentenced, they set off in search of the true perpetrators of the crime.
After falling ill to what appears to be a repressed memory Tuvok must perform a mind-meld with Captain Janeway in order to survive. The meld takes them back to when Tuvok was a junior science officer aboard the USS Excelsior under the command of Captain Hikaru Sulu.
With the crew stranded on a barren planet, and the ship controlled by the Kazon, it's up to Tom Paris, Lon Suder, and The Doctor to retake Voyager and rescue their crewmates.