Janeway and Tuvok work aboard a Borg cube with a Borg spokesperson, Seven of Nine, but the ship is attacked and sacrifices itself to save Voyager to combat the new alien threat. The new weapon proves successful, however, and the Borg leave Voyager alone once Seven of Nine's link to the collective is severed.

As Seven of Nine becomes increasingly human when the Doctor removes her Borg implants, Kes begins to evolve into a higher state of being and becomes a threat to the ship. Janeway attempts to help both women reintegrate, but ultimately must put Seven in the brig and allow Kes to leave the ship forever.  As Kes leaves she gives her former crewmates an incredible gift.

As Lieutenant Torres reluctantly faces the Day of Honor, an ancient Klingon ritual which requires examination of one's behavior, the U.S.S. Voyager is forced to eject the warp core, and she and Paris must launch a shuttle to tractor it back. Soon, the U.S.S. Voyager is ambushed by the Caatati, a race almost completely assimilated by the Borg, who demand Seven of Nine as ransom. When the Caatati attack the shuttlecraft, Torres and Paris are left suspended in space and prepare to die, prompting Torres to confide to her crewmate that she loves him

Chakotay is shot down on a planet in the midst of a bloody civil war. Taken in by friendly humanoids, he comes to share their hatred of their beastly-looking enemies. It is those enemies, however, with whom Voyager makes contact, learning that Chakotay's experiences are not what they appear to be.

Voyager is contacted by an alien hologram, the sole survivor of his ship's complement. When Torres and the Doctor investigate, they realize that the alien matrix isn't quite stable...not only is it inconsistent, but the hologram seems to be psychotic, a would-be murderer of all organic lifeforms.

Seven begins to hallucinate a large bird following her on a ship with hostile Borg, and is driven to steal a shuttle to follow a homing beacon which is activating her Borg implants. Tuvok pursues her into hostile space and the two find The Raven, the ship in which Seven's parents traveled to the Delta Quadrant, and the place where she was assimilated.

A species of superior aliens conduct grisly experiments on the crew, making them behave erratically and suffer health problems, and only Seven of Nine has the ability to perceive them.

The Krenim Imperium, a race with the ability to alter timelines, transforms the Delta Quadrant and involves Voyager in a deadly temporal war which sees the ship devastated by attack after attack and Captain Janeway pushed to breaking point.

While Chakotay and Paris work on the Krenim ship to stop any further temporal incursions, Janeway seeks allies to help rescue her crew and restore the timeline.

On a planet of telepaths, Lieutenant Torres is arrested when a violent thought from her mind causes another man to commit a crime. Investigating the seemingly open and shut case, Tuvok soon finds himself embroiled in a black market for thoughts and must use his own mental control to escape.

When aliens steal technology from Voyager, Janeway works with a holographic Leonardo Da Vinci - who has also been stolen, by way of Doc's portable emitter - to find and salvage the computer processor.

Neelix dies in a shuttle accident but is revived by Seven of Nine, who uses her nanoprobes to restore his vital signs. But he finds his faith in the afterlife shaken by the experience, and becomes despondent.

Crewmembers have nightmares about an unknown alien which threatens the ship; Chakotay must use his spiritual techniques to combat them.

A Hirogen relay station allows Voyager to send the Doctor to the Alpha Quadrant, where he finds himself on an experimental shuttle that has been overtaken by Romulans. Working with that ship's EMH, he tries to defeat the enemy and get a message to Starfleet.

Seven of Nine and Lieutenant Tuvok are captured by the Hirogen and realise the full horror of how the race treat other species, the crew receives messages from home via their relay system.

The Hirogen pursue a member of Species 8472 onto Voyager, where Janeway must decide whether to turn the deadly alien over to their mutual enemy and save her crew, or show compassion for it and put her own people in danger of becoming Hirogen prey.

Seven of Nine recalls repressed memories of having been assaulted by a member of a race of aliens with whom Voyager has been trading. With a man's life at stake, Tuvok soon realises that all may not be as it first appeared.

The Hirogen take over Voyager and force the crew to participate in violent scenarios on the holodecks in order to study both their behavior and the technology; crewmembers lose their memories and reenact scenes from Klingon history and World War II.

While Janeway and Seven break out of the World War II scenario and try to stop the Hirogen, Chakotay and Paris lead the Allied forces against the Nazis.

An alien takes over Tom Paris' body, gets him drunk, behaves rudely towards B'Elanna, and makes him waste even more time on the holodeck than usual. When the crew gets suspicious, he takes over Janeway's body instead.

Voyager comes to a standstill when the computer detects extremely powerful Omega radiation in the vicinity, triggering an unknown Starfleet protocol which the captain must implement.

Chakotay meets a woman who claims that they fell in love weeks before, but he has no memories of the event. He soon discovers her race has a technology which wipes the memory of all those who encounter them and must make a difficult decision when she asks for asylum.

Hundreds of years in the future on a planet in the Delta Quadrant, the Doctor's backup module is recovered by a race which believes he can shed light on Voyager's devastating intervention with their planet's history.

In a desperate search for deuterium, Voyager sends Tom and Harry down to a deadly Demon class planet, where they disappear and then return...in duplicate.  However when they come aboard Voyager they find the atmosphere poisonous to them.  With the "silver blood" on the planet showing signs of sentience, and Voyager sinking into the planets crust, Harry communicates with Janeway as the spokesperson of the new entity that Voyager's crew helped to create.
 

In order to pass through a dangerous nebula, the entire crew is put into stasis, leaving only Seven of Nine - who is immune to the deleterious effects - to fly the ship.

An alien translator decodes the message from Starfleet Janeway received from the Hirogen relay and leads the crew to an experimental ship which Starfleet has provided for their journey home.  They soon discover, however, that the friendly translator is not who he appears to be, and he is determined to avenge his race's annihilation which he blames on Captain Janeway.