Stardate: 50023.4. Voyager is captured by the Kazon and the crew are dumped on a planet in its early stages of evolution. As only Tom Paris and Lon Suder have evaded capture, it's up to them and the EMH to come up with a plan to retake the ship.
Tuvok experiences brain-damaging flashbacks to his service on the USS Excelsior under Captain Hikaru Sulu. He and the captain attempt to find the reason for the flashbacks, believed to be a suppressed memory, through a joint mindmeld. Special guest stars: George Takei and Grace Lee Whitney.
Tom Paris and Harry Kim wrongfully accused, convicted and incarcerated in an unguarded Akritirian prison. Tom gets stabbed trying to protect Kim, leaving him to try to find an escape plan alone. Meanwhile, Voyager is trying to find a way to prove their innocence.
Voyager encounters a swarm of ships while trying to take a shortcut through a space belonging to a hostile species, while the Doctor begins to experience memory loss.
The crew encounters the Delta Quadrant terminus of the Barzan wormhole...and the two Ferengi from the Star Trek: The Next Generation episode "The Price" now posing as gods on a nearby planet.
B'Elanna experiences vivid dreams. Which at first glance, transforms from a forbidden love affair to an increasingly dangerous path, leading to an alleged coverup concerning a planet-wide genocide.
Kes is left comatose after contacting an energy field around a rock, forcing Janeway to embark on a spiritual quest to find a cure.
A 29th century timeship causes a time paradox when it accidentally sends itself and Voyager to two different periods in 20th century Earth.
Stardate: 50312.5. While trying to rescue Paris and Tuvok, Torres and Chakotay are captured by a gang of weapons smugglers who believe that they are from the government.
Stardate: 50348.1. A dying warlord transfers his consciousness to Kes’s body and uses her to stage a bloody coup on his home world.
Stardate: 50384.2. Q begins courting Captain Janeway, claiming that her having his child is the only way to end a civil war wracking the Q Continuum.
Voyager answers a distress call from a mining colony about a viral outbreak that manages to sneak onto Voyager through the transporter, leaving only Janeway and the Doctor to stop it.
Stardate: Unknown. Voyager arrives at the dangerous and uncharted Nekrit Expanse. Neelix, feeling useless now that he can’t guide them, reaches out to a shady contact to find the crew a map.
Stardate: 50460.3. Ensign Kim asks for Tuvok’s help controlling his emotions when he finds himself desperately in love with a holodeck character.
Janeway appears to be trapped in a time-loop with different events, but all ending in her death.
Vulcan crewmember Vorik passes on the Pon farr to B'Elanna. Meanwhile, seemingly uninhabited planet Sakari is explored. After ruins are discovered, and a few survivors are found underground by the crew, it becomes obvious that local culture was destroyed by invaders. Remains of one of the invaders are found and identified - they were Borg.
Stardate: 50614.2. During an away mission, Chakotay discovers a Federation hailing signature coming from an alien planet. After landing, he learns that all is not peaceful, and those helping him have not been entirely honest about their true origins.
Stardate: 50693.2. When the doctor tries to improve his personality by incorporating the psychological profiles of famous and historical people, he is overwhelmed by their dark sides and begins exhibiting signs of a split personality, one the regular doctor, and the other dark and evil. Kes asks to leave Voyager when they encounter a race with vast knowledge of the region of space they are currently exploring.
Stardate: Unknown. Neelix is pushed to the limits when Tuvok's attitude becomes too much to bear while the pair is on an away mission to help evacuate a Nezu planet, which is being bombarded with asteroids.
Stardate: 50732.4. 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.
Stardate: 50973. 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.
Stardate: 50863.2. 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.
Stardate: Unknown. 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.
Crew members are replaced one-by-one with aliens from an unknown race.
B'Elanna Torres discovers a holodeck program where Chakotay and the Maquis rebel against Janeway.
Voyager must pass through Borg space, only to discover a new alien race that is even deadlier than the Borg.