Voyager encounters a floating truck in space and finds a number of human abductees from Earth circa 1937, including Amelia Earhart. They learn that the humans overthrew their captors on the planet and have established a civilization which Voyager's crew is invited to join.

When Chakotay takes a shuttle to perform a ritual in honor of his father's death, he is imprisoned by the Kazon. He escapes with the help of a boy who is scheduled to be executed for failing to kill Chakotay, and offers to risk his life to restore the young Kazon's honor. This episode features the first of countless shuttles which Chakotay will lose over the next several months.

On a nearly-destroyed Voyager where he has freedom to move about, the Doctor is told that he is in fact Louis Zimmerman, creator of the EMH, and has become trapped in a holodeck simulation he was running. Kes is his wife, and Reginald Barclay his programmer. Eventually the real Chakotay is projected into the simulation to inform the Doctor that it is Voyager's holodeck which is malfunctioning, and the Doctor will be destroyed if he can't stop the program.

Kes enters the elogium, the Ocampan equivalent of going into heat, and becomes desperate to have a child. While she tries to decide whether she wants to mate with Neelix, Janeway and Chakotay attempt to fight off the swarm of aliens which triggered Kes' condition and discuss the hazards of crew fraternization.

Kim awakens to find himself in San Francisco, living with his fiancé, never having been assigned to Voyager. A little investigation reveals that a meddling alien took him out of his appropriate time stream, so he struggles to get back with the help of Tom Paris, who in this reality remained a criminal.

Voyager encounters a spatial anomaly which distorts the ship from the inside out. When Janeway comes into contact with it, she is rendered incoherent, so Chakotay takes command and must decide whether to follow Torres or Tuvok's conflicting ideas for saving the ship.

Paris and Neelix beam down to "Planet Hell" in search of supplies and encounter a baby alien, which they nurture until its mother returns for it. They also fight over Kes and then bond.

Upon entering Bothan space, the crew begins to see hallucinations. Janeway first believes that her holonovel has gone berserk, then encounters her lover Mark; Tuvok sees his wife, Harry his girlfriend, Paris his father; Torres thinks she's making love with Chakotay. Kes proves resistant to the alien and saves the ship.

Chakotay's away team finds a marking very similar to one used by Chakotay's own tribe. When he experiences flashbacks from his own youth and decides to investigate, he meets an alien who claims that Chakotay's tribe were seeded on Earth by a group of space faring wanderers.

Voyager encounters an array similar to the one which stranded them in the Delta Quadrant, and discovers long-lived Ocampa living on it. One of the Ocampa teaches Kes to unlock her psychic potential and puts the Caretaker's companion in touch with the ship, but she is bent on destroying it.

When a group of Kazon under Seska's influence lead a raid on Voyager to steal technology, Chakotay steals a shuttle and goes off in pursuit. He destroys the stolen materials but is taken captive and tortured by Seska before Voyager rescues him, thus losing another shuttle. Seska leaves him a message beacon to inform him that she's impregnated herself with his DNA.

Janeway is shot during an away mission and taken in by Caylem, a man who mistakes her for his daughter. While Voyager attempts to negotiate with the aliens for the release from prison of the rest of the away team, Janeway leads a raid on the prison with Caylem's help and frees her crew.

Voyager encounters a race of robots who do not have the ability to reproduce themselves. When Janeway refuses to let Torres build a prototype for them, the robots capture her and force her assistance.

After a Kazon attack, Chakotay proposes that Janeway ally Voyager with one of the Kazon sects for protection. She reluctantly opens negotiations, then makes contact with the Trabe, a historical enemy of the Kazon, now being persecuted by them.

Paris attempts to travel in a shuttle at Warp 10 and successfully breaks the barrier, but then he begins to mutate into an amphibian and his tongue falls out. Though the Doctor devises a treatment, Paris escapes, kidnapping Janeway and forcing her to transform as well.

An unstable Maquis crewmember murders a Starfleet engineer. When an investigation points to the perpetrator, Tuvok attempts to help him gain control of his emotions via a mind meld, but is caught in the Betazoid's dark thoughts to the extent that he becomes a risk to the crew himself.

Voyager encounters a Cardassian missile which Torres had reprogrammed for the Maquis, which was apparently drawn into the Delta Quadrant with them. The missile is malfunctioning and has aimed itself at a large civilian population. While Torres attempts to disable her work from within, Janeway plans to blow up Voyager in the missile's path.

Voyager inadvertently frees a member of the Q continuum from confinement within an asteroid, where he was placed to prevent himself from committing suicide. Q appears and Janeway holds a hearing to determine whether or not the other Q will be permitted to remain free and kill himself if he wishes.

Voyager rescues a critically ill Vidiian woman who is given a holographic body by the Doctor while he treats her. They begin to fall in love, but the woman must return to her diseased-ravaged body, and she tries to sabotage the Doctor's work because she thinks death would be preferable to such an existence.

Having suspected that there was a traitor on board sending messages to Seska, Tuvok and Janeway send Paris undercover as a defector, but Neelix's journalistic meddling threatens to blow the scheme. Though Chakotay is angry when he learns that he was left out of the plan, they successfully track down their betrayer, who is killed by Neelix in a fight in engineering.

Voyager encounters a divergence field and splits into two identical ships, one damaged and one not.  Janeway must work together with her counterpart from the other Voyager or both ships will be destroyed, if not by the anomaly then by the nearby Vidiians who would love to take advantage of Voyager's predicament.  

While Janeway opens a dialogue with an alien race, Tuvok's shuttle crashes on one of their moons, where he encounters a group of children who have apparently been left as sacrifices to an unseen menace. He tries to protect them, but learns that they are not what they seem.

When Torres and Kim enter a matrix linking several unconscious aliens, they discover that Fear holds the aliens mentally captive. He kills one of the aliens to demonstrate his power and tortures Kim, but Janeway sends a holographic projection of herself into the matrix and shuts Fear down.

Coming back from an away mission to gather nutritional supplements, a transporter malfunction merges Tuvok and Neelix into one entity. Janeway is left with a difficult decision—whether to allow this new entity, Tuvix, to live or separate him and get her two friends back.

Stranded with an incurable virus, Janeway and Chakotay begin to make a new life together on a lush planet. Meanwhile, the crew pressures Tuvok to make contact with the Vidiians in the hope that they can cure the senior officers.

When Seska sends a message to Chakotay that the Kazon plan to make their son a servant, Voyager sets out to rescue the baby. The message turns out to be a trap, however, and the Kazon take the ship, stranding the entire crew on an inhospitable planet with volcanoes, large reptiles, and hostile aliens.