With the crew stranded on a barren planet, and the ship controlled by the Kazon, it's up to Tom Paris, Lon Suder, and The Doctor to retake Voyager and rescue their crewmates.
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. Onboard Voyager, Tuvok, who is now in command, faces a near mutiny.
A transporter accident merges Tuvok and Neelix into one person.
An accident in a plasma cloud creates a duplicate Voyager after they are attacked by the Vidiians.
After weeks of erratic behavior, Tom Paris leaves Voyager and joins a Talaxian convoy.
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.
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.