Stardate: 52081.2. Traveling through a large area of space completely devoid of stars and civilizations, the Voyager crew copes with the prospect of long-term isolation.
The Doctor's mobile emitter is damaged while beaming back from an away mission, merging with Seven of Nine's Borg nanoprobes and the DNA of a male Ensign to create a 29th century Borg.
Stardate: Unknown. In order to retrieve a probe stuck in a hazardous atmosphere, Tom Paris designs a new type of shuttlecraft named the 'Delta Flyer'. Torres begins to exhibit reckless behavior by engaging in dangerous holodeck programs.
Stardate: Unknown. The crew discovers an outpost manned by a group of Species 8472, who have taken human form as a training measure for an invasion of the Alpha Quadrant.
Stardate: Unknown. While Voyager searches for the crew of the crashed Delta Flyer carrying Tuvok, Paris and Ensign Wildman, Neelix must keep Naomi occupied. When it is discovered that Samantha is badly injured, he must decide how much he should tell her daughter.
Stardate: Unknown. In the future, Harry Kim attempts to correct a mistake he made 15 years earlier, which had resulted in the loss of Voyager during use of experimental engine technology.
When Voyager brings aboard an advanced piece of Borg technology from a salvaged Borg cube, Seven of Nine begins to take on the personalities of the people assimilated by the cube.
Stardate: Unknown. A moral dilemma arises when the Doctor is forced to consult the specialized medical database of a Cardassian war criminal in order to save Torres' life.
Stardate: Unknown. Tom Paris is demoted to ensign and is sentenced to thirty days in the brig for disobeying orders. While serving his sentence, Tom writes a letter to his father about the events that led to his demotion.
Stardate: Unknown. When trying to transport illegal refugees through the territory of a xenophobic civilization, Janeway must put her trust in a defector who offers his help.
Stardate: Unknown. A gap in The Doctor's memory uncovers clues to a mystery involving the nature of his existence.
Stardate: Unknown. Trans-dimensional photonic lifeforms become entangled in a war with the characters from Tom Paris' "Captain Proton" program after mistaking Voyager's holodeck for reality.
Stardate: Unknown. Stranded on a planet with little hope for rescue, Tuvok and Paris are befriended by a woman who becomes enamored with Tuvok.
Stardate: Unknown. The Voyager crew is lured into a giant space creature that consumes starships as food, and only Seven and the Doctor may have the ability to save the ship.
Stardate: 52619.2. When Janeway hatches a daring plan to steal technology from a crippled Borg ship, Seven is coerced into returning to the Borg collective.
Stardate: Unknown. Unable to resist his strong feelings for an alien woman, Ensign Kim breaks Starfleet protocol and engages in a torrid affair that lands him in hot water with the captain.
Kim finds love when the crew encounters a Varro generational ship that needs assistance repairing its warp drive.
Lt. Torres and Ensign Paris get married; the crew discover they aren't who they think they are while trying to resolve why subspace radiation is causing them and Voyager to disintegrate. Reference to Season 4 episode "Demon"
Stardate: Unknown. With Voyager pinned down by a fleet of bounty hunters, Janeway receives an offer from a group of geniuses infamous for solving unsolvable problems but asking unconventional prices.
Stardate: Unknown. An accident on a Malon freighter becomes a countdown to an explosive toxic-waste disaster, and preventing the explosion depends on Torres' ability to take control of a volatile mission.
The crew responds to a distress call from Malon escape pods contaminated with radiation.
Stardate: Unknown. Captain Janeway relates the story of her distant ancestor Shannon O'Donnell during the construction of the Millennium Gate on Earth during New Year's Eve 1999. She must convince the last holdout, local bookstore owner Henry Janeway to approve the plan.
Stardate: Unknown. The crew of a time ship from the future recruits Seven to attempt preventing Voyager's forthcoming destruction.
Stardate: Unknown. After Kim beams an alien missile onboard Voyager it links up to the Doctor's systems and requests that it is allowed to complete its mission of mass destruction.
The crew rescues a device with artificial intelligence embedded in rock, that then proceeds to take control of The Doctor and reveals itself to be a weapon of mass destruction.