Stardate: 52081.2 - Voyager comes to the aid of a warring species as Captain Janeway reflects on the decisions she has made during their time in the Delta Quadrant and their outcomes.

A transporter accident merges some of Seven Of Nine's Borg nanoprobes with the Doctor's 29th Century holo-emitter to create a 29th Century super-Borg.

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.

The crew of Voyager discover a simulation of Starfleet Headquarters being run by Species 8472 being used to practice launching an assault on the Alpha Quadrant. With the aid of regular doses of drugs, Species 8472 are able to shape-shift into human form.

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.

Voyager uses new quantum slipstream technology in an attempt to get home, but a miscalculation causes the ship to crash into an ice planet. Fifteen years later, the sole survivors, Chakotay and Kim, steal the Delta Flyer in an attempt to send a message back in time and avert the disaster, however, Captain Geordi LaForge is determined to stop them at all costs.

After encountering a piece of Borg technology known as a Vinculum which connects drone's minds together, Seven of Nine begins exhibiting the personalities of people that she assimilated as a member of the collective. Soon, they become so strong that they may overwhelm Seven's own personality.

When an alien attaches itself to B'Elanna's nervous system, the Doctor enlists the help of a holographic recreation of the Cardassian Dr. Crell Mossett. She refuses all treatment when the Bajoran crew informs her that this doctor was responsible for sadistic war crimes during the occupation.

When Voyager encounters a planet entirely of water they discover that the forcefield maintaining its integrity is breaking down. Tom Paris directly disobeys orders in an attempt to save the planet, which results in him being demoted to Ensign and placed in the brig for thirty days.

While traveling through Devore space, Captain Janeway must hide all telepaths on board in transporter stasis as telepathy is illegal under Devore law. After Voyager is repeatedly searched, the leader of the investigations requests asylum and wishes to defect.

The Doctor discovers that his short-term memory has been altered with some events being deleted, so he launches an investigation into whom or what could be responsible. When he sets a trap and the culprit is caught, he is shocked at who it is and why they're doing it.

Photonic energy life forms mistake the characters in Tom's holonovel for real people. The holodeck characters interpret this as an attack, and soon Dr. Chaotica tries to wipe them out. The only person that can stop him is Captain Janeway in the role of Queen Arachnia of the Spider People.

When Tuvok, Paris and the Doctor are pulled into a planet by its intense gravity and crash, they wait to be rescued. From their perspective, many weeks have passed with no contact from Voyager, while on board, only a few hours have passed as they plan a rescue attempt.

The discovery of a wormhole leading directly to Earth elates the crew beyond belief, but Seven Of Nine remains unconvinced that this is real. To help her cause, she recruits Naomi Wildman, the Doctor and an alien pilot named Qatai to stop the ship from entering.

Stardate: 52619.2 - After defeating a Borg ship, Captain Janeway decides to launch an attack on another damaged Sphere to steal a trans-warp coil. However, as the crew prepare for their heist, the Borg Queen is secretly aware of the entire plan.

After defeating a Borg ship, Captain Janeway decides to launch an attack to steal a trans-warp coil to shorten Voyager's journey home. The Borg detect her plan, and access Seven Of Nine's neural transceiver to deliver an ultimatum: re-join the collective or the ship and its crew will be assimilated. If she agrees, the ship will be guaranteed safe passage through Borg space.

Without medical clearance, Kim becomes involved in a love affair with a member of the Varo species. Problems arise when they become biochemically interdependent after the incident.

After Paris and Torres tie the knot, the ship and its crew start to disintegrate on the molecular level.

While boxing on the holodeck, Chakotay is contacted by a telepathic species. However, prolonged communication may leave him insane or braindead.

Voyager is ambushed by a race known as the Hazari with no way of escape. Soon, an alien 'Think Tank' arrives with an answer to the ship's problem and all they ask in return is Seven of Nine.

After encountering a damaged Malon freighter, a repair crew from Voyager tries to contain a toxic chemical leak that threatens a nearby inhabited planet. Before they embark on the mission, two crewmen from the ship warn them about the 'Angel of Decay' that wreaks havoc on board the ship.

The Doctor tries to introduce Seven of Nine to the concept of dating. After a disastrous first date the Doctor personally guides her, but he soon realises that he is falling in love with her.

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.

When Voyager is destroyed, Captain Braxton of the 29th Century Timeship Relativity contacts Seven of Nine to travel back in time and discover who planted the 'temporal disruptor.' However, she must do this without being discovered by the past Janeway.

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.

Voyager encounters another Federation starship, the Equinox, commanded by Captain Ransom, which was also abducted by the Caretaker. However, a terrible secret is exposed by the Doctor and Captain Ransom steals Voyager's technology along with Seven of Nine and the Doctor as hostages.