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.
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.