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An accident in a plasma cloud creates a duplicate Voyager after they are attacked by the Vidiians.
A suicidal Q threatens the future of the Q-Continuum when he requests asylum aboard Voyager.
After weeks of erratic behavior, Tom Paris leaves Voyager and joins a Talaxian convoy.
Seska lures Chakotay and Voyager to her, claiming that Maj Culluh is going to kill the baby she created using Chakotay's DNA, once he learns that it isn't his. Chakotay feels compelled to rescue his child, in spite of fearing it could be a trap.
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, evidence starts to suggest that he is not, in fact, the EMH on Voyager, but actually its creator, Dr. Zimmerman, stuck in a malfunctioning holodeck on Jupiter Station.
Voyager encounters a Cardassian missile ship, which Torres re-programmed while working for the Maquis. Now, B'Elanna must outsmart her own programming to disarm Dreadnought, before it destroys a planet and kills millions of innocent people.
When Captain Janeway and Chakotay contract an incurable virus they are left on a planet which shields them from its effects. While Janeway searches for a cure, she begins to form a deeper relationship with her first officer. OnboardVoyager, Tuvok, who is now in command, faces a near mutiny.
After discovering a 1936 Ford truck floating in space, Voyager follows an AM-band SOS call to a nearby planet. There, they discover a series of cryo-stasis chambers containing humans abducted from Earth during the 1930s, including Amelia Earhart and her navigator.
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, and soon begins to develop romantic feelings for her.
A spatial distortion ring puts the ship and crew at risk, as it begins to reconfigure the internal layout of Voyager.
After repairing a robot she found drifting in space, B'Elanna is abducted and forced to design a new prototype or Voyager will be destroyed.
When Ensign Lon Suder kills a crewmate, Tuvok performs a mind meld to help repress Suder's violent tendencies. However, soon after, Tuvok begins showing violent tendencies himself.
After Voyager detects a Federation probe, the Kazon-Nistrim attack and steal transporter technology. Chakotay interprets this as a personal attack, and is then captured.
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.
Harry Kim arises one morning to find he is back in San Francisco on Earth with his girlfriend Libby. He learns that in this reality, he never served aboard Voyager, but instead works in Starship Design at Starfleet Headquarters. Desperate to set things straight, the only person who can help him is lowlife Tom Paris, who has no idea who Harry is.
A transporter accident merges Tuvok and Neelix into one person.
The crew of Voyager make contact with the Caretaker's mate, Suspiria, and hope she will be able to send them home. Meanwhile, Kes meets with other Ocampa living on Suspiria's array, descended from a group that left the homeworld over 300 years earlier, who encourage her to develop her mental abilities.
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.
Tuvok and B'Elanna are captured and imprisoned after an away mission goes wrong. Janeway is knocked unconscious and is rescued by a man who believes that she is his daughter.
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.
When Tuvok crashes on a moon, he discovers three small children who believe they are about to die.
A young Kazon trying to earn his name and place among his people kidnaps and tries to kill Chakotay.
After Neelix and Paris come to blows over Kes, they find themselves trapped together on a planet dubbed "Planet Hell" and become the unwilling parents of an infant alien. They must set their differences aside and work together in order to save the infant's life, while Voyager's search mission is delayed by an alien attack.
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".
When the crew of Voyager investigate a cluster of space-borne life forms, Kes prematurely enters a stage in her life known as the "Elogium". This is the only time in her life when she can conceive a child.
Tom Paris begins evolving into a higher organism after achieving warp 10 in an experimental shuttle.