After discovering a 1936 Ford truck from Earth floating in space Voyager discovers a series of cryo-statis chambers containing abductees from Earth during the 1930's, including Amelia Earhart and her navigator.
A young Kazon trying to earn his name and place among his people kidnaps Chakotay.
When the Doctor is activated during a Red Alert, he learns that the ship has been abandoned, and that only B'Elanna Torres and an injured Captain Janeway are left on board. Soon afterwards, Lt. Barclay appears and tells him that his entire time on Voyager is an elaborate simulation, and he's really a holo-engineer by the name of Zimmerman on Jupiter station in the Alpha Quadrant, who has been trapped on a holodeck for six hours. If he does not destroy Voyager's warp core and end the program soon he will die.
When the crew of Voyager investigate a cluster of space-borne life forms, Kes is forced into a stage in her life known as the 'Elogium.' This is the only time in her life when she can have a family.
Harry Kim arises one morning to find he is back in San Francisco on Earth with his girlfriend Libby. In order to help him restore reality, he enlists the help of a shady figure in France by the name of Tom Paris, who has no idea who Harry is.
A spatial distortion ring begins to reconfigure the internal layout of Voyager. With the crew unable to get to vital systems, and the captain injured after coming into contact with the anomaly, the ship is slowly twisted as the ring implodes and endangers the crew.
When Neelix and Paris find themselves trapped on a planet dubbed 'Planet Hell', they become the unwilling parents of an infant alien that is near death. In the meantime, a ship appears and begins attacking Voyager.
Captain Janeway starts seeing characters and objects from her holo-novel around the ship. Soon afterwards the crew begins entering a catatonic state one by one, while only Kes and the Doctor remain unaffected.
Upon discovering a cultural symbol drawn in the ground on a planet that was used by his ancestors to 'heal the land', Chakotay tries to contact the beings his tribe called the 'Sky Spirits.'
The crew of Voyager make contact with the Caretaker's mate, Suspiria. Kes meets with the descendants of other Ocampa on Suspiria's array that left the homeworld over 300 years ago. Soon, her mental abilities begin to grow to a point where she can no longer control them, and nearly kills Tuvok in the process.
After Voyager detects a Federation probe, the Kazon Nistrim attack and steal some transporter technology. Chakotay interprets this as a personal attack, and is then captured.
Tuvok and B'Elanna are captured and imprisoned after an away mission to obtain a chemical vital to Voyager's systems from a black market go wrong. Janeway is knocked unconscious and is rescued by a man who believes that she is his daughter.
After finding and repairing a robot found drifting in space, B'Elanna is abducted and forced to design a new prototype or Voyager will be destroyed.
In order to stop attacks from the Kazon, Captain Janeway finds herself being forced to make an alliance with the more powerful Kazon sects. When negotiations fail, their only chance is to ally themselves with the race that used the Kazons as slaves in the past, called the Trabe.
Tom Paris begins evolving into a higher organism after achieving warp 10 in an experimental shuttle.
In order to help out Lon Suder, a psychopath who killed a crewmember, Tuvok performs a mind meld. Soon after he begins showing violent tendencies, which develop until he loses control.
When Voyager encounters a Cardassian missile ship in the Delta Quadrant named 'Dreadnought', B'Elanna must disarm it before it destroys a planet with millions of innocent people.
A suicidal Q threatens the future of the Q-Continuum after he requests asylum aboard Voyager.
After receiving a Vidiian patient who is about to die from the Phage, the doctor transfers her consciousness into the ship's computer and creates a holographic body. He soon finds himself becoming deeply attracted to her.
After weeks of erratic behavior, Tom Paris leaves Voyager and joins a Talaxian convoy.
An accident in a plasma cloud duplicates Voyager after they are attacked by the Vidiians. During the aftermath, the ship is severely damaged, Ensign Wildman's baby dies and Harry Kim is sucked into space through a hull breach.
When Tuvok crashes on a moon, he discovers three small children who believe they are about to die.
The crew of Voyager encounters a planet that has recently entered an ice age. They discover a series of stasis chambers where a small group of people are mentally connected to an artificial environment that turned horribly wrong.
A transporter accident merges Tuvok and Neelix into one new being who calls himself 'Tuvix.'
When Captain Janeway and Chakotay contract an incurable virus they are left on a planet that shield them from its effects. While Janeway searches for a cure, she begins to form a deeper relationship with her first officer. Onboard Voyager, Tuvok, who is now in command, faces a near mutiny.
Voyager receives a distress signal from Seska, who claims that Maje Cullah is going to take her baby away from her, a baby she says is Chakotay's. Chakotay is skeptical, but can't take the risk of abandoning his child, should it really prove to be his.
Janeway authorises a mission to rescue Chakotay's child and the ship moves deep into Kazon Nistrim territory. However: was Seska for real, or is this all an elaborate trap?