The Voyager crew are assaulted in the form of nightmares. An alien species, functioning only in a dream world, disables the crew and traps them in a shared dream. Chakotay strives to stay awake and help The Doctor disable the aliens' hold on the crew, all while wondering if he is still dreaming.
After Voyager is captured by the Hirogens, the ship is turned into a massive holodeck so that the Hirogens can hunt members of the crew who have been fitted with new identities in various scenarios based upon Federation history.
Bored with his daily routine, Tom Paris finds a refreshing friendship with a visiting alien willing to share a new method of propulsion with Voyager. Unwittingly, Tom finds trouble when his new friend swaps bodies and delivers him to authorities ready to charge Tom with the aliens' crimes. Meanwhile, the alien in Tom's body makes waves in Tom's personal and professional relationships on Voyager.
Voyager's sensors detect a rare particle theoretically capable of damaging subspace and nullifying warp travel. Under a classified directive known only to Starfleet Captains and above, Janeway leads Voyager on a mission to destroy all traces of the particle. Seven of Nine is hesitant to destroy the Omega particle, remembering the Borg revered it as the embodiment of perfection.
An alien woman requests asylum aboard Voyager, stating she has been aboard recently and she and Chakotay fell in love. She claims her race wants to keep themselves concealed from other races and have ways to forget contact with her species. Once an agent charged with returning fugitives to her homeworld, she is now being hunted by her former colleagues for revealing her race's secrets.
When The Doctor's back-up module is found, his program is brought on-line for the first time in seven hundred years. In the future, Kyrian Museum of Heritage teaches a history that writes Voyager as playing a detrimental role in beginning their Great War with the Vaskans. The Doctor is the only living witness and sets the record straight, but the new "facts" give way to old tensions from the formerly warring races and the museum curator and The Doctor find themselves amidst violence and destruction instead of the peace and understanding they hoped for.
Desperate to replenish the ship's power resources, Voyager seeks out a deuterium signature on a class "Y" a.k.a. "Demon Class" planet. After nearly being lost, Paris and Kim are thought to be "bioformed" to the planet's atmosphere. Further investigation uncovers a strange life form which after making physical contact with the away team, has developed self-awareness and will do anything to keep it.
An unavoidable poisonous nebula forces the entire crew into stasis chambers - all except the unaffected Doctor and Seven of Nine, who must fight her nearly life long "collective" mentality to handle being alone for over a month while combating ship-wide failures, a strange alien intruder, and her own fears of individuality and loneliness.
After a Starfleet rescue ship, the Dauntless, is located, an alien visitor interprets a damaged data stream from Starfleet Command. The ship features a novel "slipstream" drive that offers quick trip home to earth. After her initial delight is tempered by suspicion and Seven of Nine proposes to remain in the Delta Quadrant Captain Janeway re-interprets the message and accosts the alien whom takes her and Seven-of-Nine away on the Dauntless. He reveals that her assistance to the Borg against Species 8472 led to Borg domination of a large portion of the Delta Quadrant ...
Crew morale hits an all-time low when Voyager must spend two years crossing an expanse devoid of any star systems or signs of life. As Captain Janeway is forced to reflect on the choice she made stranding her crew in the Delta Quadrant, little does she know, she will face a similar decision when Voyager ends up in the middle of a serious conflict.
Voyager is investigating the birth of a nebula. Unfortunately, after an away mission shuttle is caught in the blast, a transporter accident during the team evacuation causes the Doctor's mobile emitter to be infected with Seven's nanoprobes. The mobile emitter starts assimilating a science lab, and creates a new drone built upon the emitter's twenty-ninth century technology.
B'Elanna Torres secretly participates in several dangerous holodeck programs. The Voyager crew works around the clock to build the Delta Flyer, hoping to beat the Malon in retrieving a lost probe from the atmosphere of a gas giant.
The crew of Voyager discover a simulation of Starfleet Headquarters being run by Species 8472. With the aid of regular doses of drugs, Species 8472 are able to shape-shift into human form. It is up to Janeway to try to convince the aliens that Starfleet is not a threat to them.
The Delta Flyer crash lands after encountering an ion storm. Voyager desperately tries to contact and rescue Tuvok, Paris, and a badly injured Ensign Samantha Wildman. Meanwhile aboard ship, Neelix attempts to distract young Naomi Wildman, who is eager to hear from her mother. Finding out the truth, Naomi escapes into a popular children's holo-novel.
A miscalculation by Ensign Kim causes a fatal crash during Voyager's first test with slipstream travel. Fifteen years in the future, survivors Chakotay, Kim and The Doctor attempt to send a message back in time to prevent the tragedy.
An injured cytoplasmic life-form attaches itself to Torres, tapping into her body like a parasite. Unsure of how to save his patient, The Doctor creates a holographic recreation of a non-humanoid exobiology specialist to consult the case. The consult is going well until Torres refuses treatment when it is made known the Cardassian specialist was responsible for tortuous experiments resulting in the deaths of thousands of Bajorans.
Voyager passes through a sector of space controlled by race which is deeply suspicious of telepathic lifeforms. Tuvok and others force the Voyager crew to develop a novel approach in order to pass through safely.