Seven of Nine, the Borg drone that Voyager severed from the collective, tries to resist as her natural human physiology tries to regenerate. It's up to Captain Janeway to convince her to embrace her humanity and join the Voyager crew. Meanwhile, Kes' telekinetic powers grow to such a point that she can no longer control them. In order to prevent Voyager from being destroyed, she decides she must leave the ship.
The Klingon holiday known as Day Of Honor comes around again and this year B'Elanna Torres decides to embrace her Klingon heritage and participate in a series of ritual endurance tests. But blood pie and painstiks are the last thing on her mind when an emergency necessitates ejecting Voyagers warp core. Torres and Tom Paris are sent in a shuttlecraft to retrieve it but the Caatati decide they want the core and destroy the shuttle. Paris and Torres don EV suits and beam off in time, only to find themselves adrift in space with little oxygen. Accepting her impending ...
Commander Chakotay's shuttle is hit by enemy cross-fire and crashes on a planet in the midst of a war. One side befriends him and attempts to help him locate his shuttle and he finds himself quickly taking sides. When he is captured by the other side, he is reminded that every army has its own story.
Voyager receives a distress call from a lone survivor on a damaged ship. When learning the survivor is a hologram, The Doctor insists on joining B'Elanna Torres who lends aid in fixing the ship. Once on the ship, Dejaren (guest star Leland Orser) expresses his hatred of "organics," and Torres discovers that the crew were not killed by a virus but instead brutally murdered, Dejaren turns on her and nearly kills her too.
Janeway is trying to gain passage through a region of space owned by a cautious and xenophobic race of aliens. Negotiations are disrupted when Seven of Nine believes that she is being contacted by the Borg and forcefully leaves Voyager to rejoin the collective and heads into the alien territory.
Voyager visits a planet with a telepathic races that outlaws negative thoughts. When B'Elanna is charged with releasing an angry thought into the society and condemned to a dangerous neurological procedure, Tuvok uncovers a black market dealing in violent thoughts.
While Janeway is visiting her da Vinci holodeck program, Voyager is mugged by transporter. They steal everything from the main computer core, to the emergency rations, even the dirty laundry! They track the property to a trade outpost. When they take a team to recover the gear, Janeway is shocked to find her holodeck character da Vinci (guest star John Rhys-Davies) - wearing The Doctor's mobile emitter living there. He believes it is America, and tells her he has been hired by the Prince as an inventor. With da Vinci's help, she gets the computer back, but the 'Prince...
Neelix experiences a crisis of faith when, after being dead for nearly nineteen hours, Seven of Nine revives him using her Borg technology. On awakening, Neelix has no memory of experiencing the Talaxian afterlife and begins to doubt everything his culture believes about the post-thanatic experience and their spiritual place in the universe. His crisis is played out with the help of Chakotay's vision quest.
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 ...