After Janeway's crew successfully infiltrates the Collective, the Borg Queen vows to stop their insurrection even if she must destroy her own kind to do so.

Seven is faced with her own mortality when her cortical node fails, and crewmembers are faced with ethical dilemmas about how far they will go to save her.

Paris and Kim volunteer to enter a race that symbolizes a peace treaty between four warring races. However, the race's peaceful intentions are undermined with plans of sabotage and murder. Torres feels she is nearing the end of her relationship with Paris. However, they work things out with surprising results.

When Maquis crewmembers begin reacting to post-hypnotic suggestions that they take over the ship, Tuvok must identify the culprit. However when it becomes clear Tuvok is also affected, Janeway faces a mutiny...

The Doctor's program is stolen and placed aboard a hospital ship where unethical treatment of patients is rampant. The Doctor struggles with his ethical subroutines as patients with more to contribute to society are given preferential treatment.

Voyager receives a transmission from the Alpha Quadrant in which a hologram of Barclay suggests a way home; meanwhile, the real Barclay discovers that his hologram has gone missing.

An alien attack forces Seven of Nine to take the Doctor's programming into her cybernetic implants, from which he can control her body. The aliens are prejudiced against holograms leaving the Doc in a very difficult position.

While in command of the Delta Flyer, Harry Kim intervenes in an alien conflict and soon learns the difficulties of being a captain. Kim's Starfleet training is pushed to the limit when he faces a mutiny from the alien crew.

A Hirogen distress call alerts Voyager to the plight of sentient holograms created from Starfleet technology, and forces the Doctor to reevaluate his loyalties.

The sentient holograms forcibly abduct Lieutenant Torres and force her to repair their captured ship. Meanwhile, the Doctor is torn between his ethical obligations as a healer and loyalty to his fellow holograms.

When an anomaly time-shatters Voyager, Chakotay leads a pre-stranded Janeway around her ship, showing her key moments in the past and future.

Against her husband's wishes, Torres seeks to remove all the Klingon genes from their unborn child. Discovering the root of the problem, Tom reassures Belanna that he will not leave her like her father did, even if they have several Klingon children.

Voyager rescues a ship carrying prisoners to their home planet for execution, but inadvertently treats the mental illness of one of the condemned.

The crew encounters a Klingon generational ship that has been roaming the galaxy for decades; its captain hails Torres' unborn child as their messiah.

With her ship trapped in a starless void and supplies rapidly dwindling, Janeway tries to forge an alliance of distrustful aliens to escape and resume her course for Earth.  Meanwhile the Doctor discovers a way to communicate with the voids only indigenous lifeform.

The crew of Voyager live as workers on an industrial planet, totally unaware of their time on Voyager.  Chakotay, Kim and Neelix, return from an away mission to find the ship abandoned and adrift in a nebula, with only the Doctor on board.  After going undercover on the planet, Chakotay, Kim, Neelix and the Doctor must  find a way to return the crew and restore their memories, while evading local authorities and a doctor who believes he is doing the right thing for his people.

While Chakotay tries to recover the crew, Janeway moves in with her new lover and the Doctor finds he enjoys command a little too much. In order for their plan to succeed, Janeway must trust Chakotay who she perceives as a criminal, and leave the new life she has begun to create for herself.

Voyager is traveling through a treacherous region of space, but Seven of Nine is distracted by a holo-program that lets her explore her sexuality with Chakotay.

When Q brings his son to Voyager to ask his godmother to parent him, Janeway tries to clean up Junior's act. Trying to impress his father, Junior causes a chain of events which wreak havoc among neighboring alien civilizations.

The Doctor writes his holo-memoirs and sells them to a publisher in the Alpha Quadrant, turning his crewmates into nasty characters in order to make points about the oppression of holograms.

Starfleet asks Voyager to retrieve an old Earth probe believed missing in the Delta Quadrant. But the probe has wreaked havoc on a local species, which takes Lieutenant Carey hostage and kills him.

Chakotay and Seven are stranded in a primitive enclave on a technologically advanced world. Janeway must decide whether to rescue her crewmembers by taking down the barrier that separates the two societies.

Neelix tries to rescue a colony of besieged Talaxians and decides to stay in the Delta Quadrant with his own species, serving as a long-distance ambassador for Starfleet.

The captain acts very strangely after returning from an away mission with the Doctor, who also acts strangely, as do Chakotay and Torres in turn. It turns out that the Doctor is taking on the personalities of other crewmembers to save the captain from a ransom demand.

A future Admiral Janeway visits present day Captain Janeway telling her of a plan to finally get the stranded crew home. The crew acts with mixed feelings when they discover they must traverse a Borg infested nebula.

In an effort to stop the destruction of the transwarp hub, the Borg Queen captures Admiral Janeway and assimilates her. But as Voyager speeds through the conduit with a Borg cube on its tail and Belanna gives birth to her new daughter, the Borg find out that it is a good idea to be careful what you assimilate.