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.
When the demon Karkull transforms the Daily Planet Building into his evil fortress, Superman must enlist the aid of the retired mystical superhero, Dr. Fate.
Seven Of Nine, the Borg drone that Voyager severed from the collective, tries to resist as her natural human physiology tries to regenerate. It's up to Captain Janeway to convince her to embrace her humanity and join the Voyager crew. Meanwhile, Kes' telekinetic powers grow to such a point that she can no longer control them.
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.
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.
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.
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.
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.
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.