Almost the entire crew of Voyager have been marooned on a desolate planet by the Kazon. Tom Paris was sent out to try and find someone who can help them. Furthermore, Lon Suder and the Doctor, who are still on Voyager, try to help.
Captain Janeway participates in a mind meld with Tuvok, who relives his experiences on the U.S.S. Excelsior under the command of Captain Sulu at the time of Star Trek VI: The Undiscovered Country (1991).
Tom Paris and Harry Kim are wrongly convicted of a terrorist bombing. Even though Janeway captures the true criminals, Tom and Harry are fitted with strange brain implants and imprisoned on a satellite. In the prison, the inmates have no supervision, no medical care, and all have implants which increase their aggressive tendencies. New prisoners and food-rations are delivered through a one-way chute. As days pass, the friends try to hold on to reality but find themselves turning on one another and taking drastic measures to survive and attempt escape.
Voyager is attacked by swarms of tiny spaceships which attach themselves to Voyager's hull. The Doctor is losing his memory and Torres activates the Jupiter Station diagnostic program run by a familiar hologram.
A timeship from the future who tries to stop Voyager gets thrown with Voyager into the twentieth century. His timeship is found in the 1960's and Voyager finds a company that has benefited from its technology exists in 1996.
Henry Starling, who made a fortune from his looting of 29th century technology from the crashed timeship, is planning a foray into the future to feed his greed. The Voyager crew must find a way to stop Starling before his attempted use of the timeship destroys Earth's Solar System. Meanwhile, while trying to rescue Paris and Tuvok, Torres and Chakotay are captured by an anti-government white supremacist militia who believe that they are feds.
Due to the death of the Q in their last encounter with Voyager, a Civil War has broken out among the Q continuum. A new Q needs to be produced and the mischievous Q known to the USS Enterprise has chosen Janeway as his mate.
Harry Kim finds himself in love with Marayna, a character from Neelix's Polynesian resort holodeck program. Seeking to eliminate the emotion, Harry turns to Tuvok, who interacts with the woman and finds himself falling for her as well. While Harry is overwhelmed with feelings of jealousy and betrayal, Tuvok realizes the persona is too real and discovers she is actually a lonely alien who can interact with passing ships through their computers.
Ensign Vorik undergoes the Vulcan mating drive known as Pon farr. The strong chemical imbalance affects B'Elanna Torres as well, leading her to irrational thoughts and behavior. Trapped in a cave, Tom Paris must try to reason with B'Elanna and get her medical attention while trying to respect his friend and deny her uncharacteristic sexual advances.
Kes falls in love on an away mission. The Doctor, seeking to expand his programming, incorporates the personalities of several historical figures. B'Elanna Torres chastises The Doctor, warning him that his program is complex and the results could be unfavorable. But, it is too late, as the Doctor develops an alter-ego; a violent, unethical personality who attempts to murder Kes' new beau.
While Ensign Kim begins experiencing bizarre DNA changes, he instinctively leads Voyager to a planet whose inhabitants claim Kim is really a member of their race and is ritualistically returning home. When his welcome seems too good to be true, Kim loses contact with Voyager and begins to uncover the alien's true intentions.
Starting near her death with no memory, Kes experiences parts of her life moving backwards through time. The Doctor develops an experimental procedure to extend Kes' lifespan beyond the Ocampan standard nine years. We see a possible future Voyager where Janeway and Torres died years ago in a great war and the survivors of Voyager were exposed to temporal radiation. The Doctor's procedure re-activates the symptoms of the radiation, causing Kes to relive moments of her life, from being elderly to her conception. In this reality, Kes and Tom Paris married and had a ...
The Doctor creates a holographic family, but B'elanna Torres thinks the Doctor's simulation is too "nice" (in a "Leave It To beaver" sort of way). She introduces some alterations to the program to make the simulation more accurate to real life: a wife who often disagrees, a rebellious teenage son, and a daughter who is sure she knows better than her doting father. When his daughter is critically injured the Doctor must make a choice, run back to his Voyager life, or face the harsh "reality" of losing a loved one.
A Voth scientist finds the remains of a Voyager crewman who died on the planet where the crew was exiled by the Kazon during the two-part episode "Basics". An analysis of the remains' DNA shows links to his own DNA. While tracking and studying the Voyager crew, the scientist and his aide are discovered; they eventually pool their knowledge and conclude that the saurian is an evolved dinosaur from a species that left Earth more than 65 million years earlier. The scientist is thrilled to be able to prove his Distant Origin theory (that his Voth race originated elsewhere...
Members of the Voyager crew clandestinely participate in a hidden holodeck program where the ship's Maquis members stage an insurrection. Word gets out and Tuvok confesses to writing the program as a training guide for security officers but never finished it because the merged crew seemed to be working well together. When Tuvok and Paris get trapped in the program, they realize that former crew mate and Cardassian spy Seska had added her own twist to the story.