Stardate: 51003.7. The Voyager crew, allied with the Borg, prepare to battle the sinister alien Species 8472. But can an alliance between opinionated individuals and a collective race of consumers survive such fundamental differences?
Kes' mental abilities develop to a point where they endanger while The Doctor and Janeway slowly help Seven of Nine cope with being severed from the Borg.
Stardate: Unknown. When Voyager is forced to eject its warp core, Torres and Paris take a shuttle to retrieve it. But when the shuttle is damaged, the two officers are forced to abandon it—and find themselves alone in space with a rapidly depleting oxygen supply.
Stardate: 51082.4. Chakotay is stranded on a planet where two races are trying to wipe each other out in a massive, planet-wide war.
Stardate: 51186.2. Torres and the Doctor assist a holographic ship's servant whose crew has been killed. Meanwhile, when Kim and Seven of Nine are assigned to work on a project together, the ensign attempts to get to know the person inside the mysterious former-Borg.
Stardate: Unknown. Seven of Nine steals a shuttlecraft and flees Voyager in an attempt to answer a mysterious homing beacon and return to the Borg Collective.
Stardate: 51244.3. When members of the crew begin suffering from bizarre mutations, Seven of Nine may be the only one who can uncover the reasons why.
Voyager creates a new astrometrics lab, which maps a new course that brings them into contact with a Krenim temporal ship that can erase things from history.
A badly damaged Voyager hides in a nebula as a skeleton crew attempts repairs; meanwhile the Krenim commander proposes a compromise to Chakotay and Tom Paris.
Stardate: 51367.2. After making contact with a race of telepaths, the Voyager crew must help defuse a volatile situation when a local citizen acts on a random, violent thought inadvertently tranferred from Torres.
Stardate: 51386.4. Janeway and the hologram of Leonardo da Vinci must work together to retrieve Voyager's main computer processor, which has been stolen by alien thieves.
Neelix dies in an attempt to sample proto-matter from a nebula. Seven of Nine helps resuscitate him using Borg nanoprobes, but Neelix, having no memory of an afterlife of any kind, experiences a spiritual crisis.
The crew becomes trapped in a shared nightmare generated by alien technology. Only Chakotay, through his Native American spiritual capabilities, can save them.
The Doctor's program is sent to an advanced Starfleet vessel via a vast ancient communications network, but he soon discovers that only he and the ship's own EMH remain to fight against Romulans who have taken over the ship and are attempting to return to Romulan space with it.
Stardate: 51501.4. As letters from the Alpha Quadrant come trickling through the communications array, the Voyager crew learns of an assortment of joyous, disturbing, and inevitable news.
Stardate: 51652.3. The crew rescues a critically injured but aggressive Hirogen hunter, who threatens to have his allies destroy Voyager if Janeway comes between him the hunt for his latest prey: a single creature from Species 8472.
After experiencing unsettling hallucinations, Seven of Nine is hypnotized by the Doctor whose analysis reveals a trader might have extracted Borg technology from Seven without her consent.
Stardate: Unknown. After having taken over Voyager, the Hirogen supply the crew members with artificial identities and subject them to violent holodeck simulations.
Stardate: 51715.2. The crew must stop an artificial holodeck rendition of a World War II battle from spilling onto the decks of the ship while simultaneously dealing with a Hirogen takeover.
An alien shuttle with a prototype propulsion system suddenly appears and requires assistance. Paris is restless and volunteers to help the pilot, Steth, repair the shuttle.
Janeway undertakes the Omega Directive, an order to destroy Omega molecules, even if it means violating the Prime Directive.
Stardate: Unknown. An alien woman who requests asylum on board Voyager claims that she was onboard the ship a month ago, and she fell in love with Chakotay.
Stardate: Unknown. 700 years into the future the Doctor must defend the crew of Voyager and set history straight when an alien race claims that the Warship Voyager was responsible for war crimes commited against their race.
Stardate: Unknown. Kim and Paris beam down to a hellish, barren planet to search for deuterium, a crucial energy source required to keep the ship running.
Seven of Nine is left alone on Voyager when a nebula's deadly radiation forces the rest of the crew to stay in stasis and the Doctor's holographic program is disrupted.
Stardate: 51978.2. When an alien helps the Voyager crew decode the mysterious encrypted message from Starfleet, the crew learns the whereabouts of a secret experimental starship that may be able to get them back to the Alpha Quadrant within a mere matter of months.