While Tom Paris rounds up Talaxian assistance, Janeway and crew struggle to survive on a world with few provisions and many threats. Meanwhile, Seska and the Kazon must fight a Voyager saboteur.

An encounter with a familiar-looking nebula causes Tuvok to experience flashbacks to a terrifying event from his childhood. A mindmeld with Janeway takes him back to his years serving under Captain Sulu on the Excelsior, where he was invaded by an alien life-form.

Paris and Kim are taken captive on a prison barge with horrific living conditions, where the prisoners are expected to kill one another off. When Janeway is unable to negotiate for their release, she captures the criminals responsible for the crime her crewmembers were convicted of, forcing them to assist her in freeing her people.

As the Doctor's program experiences a serious overload which requires his reinitialization, Voyager enters the space of a group of vicious aliens who attempt to seize the ship. The crew successfully fights them off, and Torres uses a hologram of Louis Zimmerman to rescue the Doctor.

Chakotay and Paris' away team discovers two Ferengi who came through a wormhole profiting off a local population. Janeway's plans to thwart them repeatedly backfire, until finally the captive Ferengi take back their ship and enter the wormhole themselves, moving it out of Voyager's reach.

Torres relives a lifetime of memories from a woman which perpetrated and then covered up the extermination of an entire population, one of whom was her youthful lover.

When Kes is nearly killed by an alien energy beam, Janeway undergoes a ritual to try to save her. Along the way, her own belief system is tested.

Voyager is pulled into a temporal wave and deposited near Earth circa 1996, where a 20th century man with technology from the 29th century is about to cause a cataclysm which will destroy the solar system.

While Paris bonds with a 20th century astronomer and Chakotay and Torres are taken prisoner by survivalists, Janeway attempts to stop the man who will be responsible for the destruction of the solar system.

The body of Kes is taken over by the spirit of an ancient warlord who wants to use her to retake control of his planet. Though the spirit within her attempts to seduce Tuvok and torment inhabitants of the planet, Kes fights the warlord with her mental powers.

Q demands that Janeway have a child with him to stop a civil war in the Q continuum, portrayed for her benefit as the U.S. Civil War. She refuses but offers to help negotiate a truce. Meanwhile, Q's angry former Q lover brings Voyager to the continuum to help them rescue Janeway before Q can mate with her.

Janeway returns from an away mission to find that macroviruses have incapacitated her crew and taken over her ship. With only the Doctor as an ally, she fights them off.

Panicked that his usefulness to Voyager may have come to an end, Neelix offers to trade goods stolen from Voyager for a map to upcoming star systems. He becomes entangled in an organized crime ring, and Chakotay and Paris are arrested under suspicion of murder.

A hologram becomes obsessed with Tuvok and takes control of the ship to be with him. Eventually the crew discovers that the holographic character is being controlled by a lonely woman in a nearby nebula.

Janeway and Chakotay are caught in a recurrent time loop which always ends with her death, despite Chakotay's frantic attempts to revive her. A man who appears to be her father arrives to tell her that in fact she is dead, and he has come to help her "cross over".

When Vulcan engineer Vorik tries to force Torres to mate with him, she contracts his blood fever and selects Tom Paris as the object of her desires. Unfortunately, the two are trapped together during an away mission before anyone figures out what's wrong with her.

Chakotay's shuttle is shot down on a planet where former Borg are at war with each other. Rescued by a group of pacifists who treat his injuries and give him a taste of collective existance, he asks Janeway to help them reunify the collective. When she refuses, the group which saved his life commandeer his brain to gain his assistance.

The Doctor programs his matrix with characteristics from a variety of historical and literary figures. Unfortunately, this has the effect of creating an evil personality which takes over the Doctor without warning, torturing Torres and threatening Kes.

When aliens on a meteor-besieged world ask for help from Voyager, Tuvok and Neelix are trapped together on the surface. They attempt to leave the atmosphere via an orbital tether in order to make contact with Voyager, but one of their fellow passengers is a murderer.

Harry Kim is drawn to a world of beautiful women and few men who insist that he is a descendant of theirs, taken as a fetus across the galaxy to be implanted in his mother's womb. His mutating DNA appears to confirm this story until the Doctor realizes that it did not begin to change until they passed through a certain port.

Kes finds herself living backwards in time, with no memory of who she was before she began as an old woman. In the reality she sees in reverse, she has married Tom Paris and had a child with him who in turn married Harry Kim; Janeway and Torres have been dead for years, killed during a conflict with a race that used chronoton particles to alter the timeline.

The Doctor creates a holographic family so that he can experience what it means to be organic. When Torres and Kes complain that his initial projection - a perfect family - is unrealistic, he allows Torres to program some changes and ultimately experiences painful loss.

A Saurian scientist pursues Voyager in hopes of proving his theory that his species did not evolve in the Delta Quadrant, but evolved from dinosaurs on Earth. The scientist, who takes Chakotay first as a hostage and then as a willing witness, must convince his ruling council that his findings will not be disruptive to their society.

Crewmembers from Voyager disappear and are replaced by befuddled aliens, but the crew suspects a more sinister plot. Sure enough, the aliens are moving Voyager's crew to a penal colony in preparation to take over the ship, which Chakotay sabotages before being taken himself.

Torres discovers a holodeck scenario set early in Voyager's mission, in which Chakotay leads a mutiny and takes over the ship. It proves so popular with the crew that Tuvok is convinced he must finish it. But when he tries to do so, he discovers that Seska has made some deadly changes in the program.

Voyager reaches Borg space and finds a narrow corridor free of Borg ships... but the corridor proves to hold an even more deadly menace. Janeway proposes an alliance with the Borg to get through the space and combat the new threat, over Chakotay's vehement objections. She beams over to a Borg cube, which is attacked, dragging Voyager away as it flees.