Chakotay is told his son has been taken by the Kazons, during the process of trying to rescue him Voyager is taken by the Kazons after the crew looses the ship in a running battle with the Kazons.

After Captain Janeway and Chakotay contract a deadly virus, they are set down on a small planet so the rest of the crew will not become infected.

Stardate: 49655.2 While returning from an away mission, a transporter accident merges Tuvok and Neelix into one new being with the personality of both combined. He calls himself "Tuvix." But the  Doctor's search for how to restore their original forms causes a moral dilemma as Tuvix does not wish to be terminated.

The crew of Voyager discovers a world with technology and no people. They then determine that the planets inhabitants are in hibernation in order to protect themselves from a natural disaster.

After Tuvok crash lands on a moon that is considered sacred, he attempts to save three abandoned children,  while also repairing his shuttle.

While trying to avoid the Vidiians, Voyager travels to a region of space that will disguise them from their sensors. Subsequently, an onboard disaster occurs while Ensign Wildman is having her baby, which causes problems for the Doctor.

Lt. Paris leaves Voyager to travel with a Talaxian convoy claiming to not fit in with Voyager's crew. Neelix later suspects Lt. Paris of being a traitor to Voyager when he decides to become a investigative video journalist.

Voyager rescues a dying Vidiian and during the process of trying to save her life, the Doctor's adaptive program allows him to experience romantic feelings for the first time. Lt. Paris starts objecting to his treatment on Voyager and ends up assaulting Chakotay.

While taking a sample of a strange space phenomenon, Voyager brings a Q aboard. This in turn causes the original Q to come onboard, demanding that the new Q come back to the Q Continuum with him.

Stardate: 49447. Voyager encounters Dreadnought, an advanced, self-aware Cardassian missile also drawn into the Delta Quadrant that B'Elanna Torres reprogrammed during her time in the Maquis. The missile, believing it is still in the Alpha quadrant on its Maquis mission, is on course to destroy Rakosa V, an inhabited world of millions. Now, B'Elanna must outsmart her programming to disarm Dreadnought before it reaches its objective.

After a crewman is murdered, Tuvok decides to try and understand what drives a person to commit violent crimes. He uses a mind meld on the killer and starts to have violent tendencies of his own.

Paris experiments with breaking the warp 10 barrier. Once transwarp is achieved, Lt. Paris starts to undergo a strange transformation which places his life in danger.

Captain Janeway reluctantly tries to form an alliance with the Kazons and their longtime enemies in order to strengthen Voyager's position in the quadrant.

Lt. Torres and Ensign Kim help a humanoid robot that is discovered by Voyager. Torres is then kidnapped by the robot and its fellow robots, who threaten to destroy Voyager unless Torres helps them.

Janeway is forced to rely on her own devices when Torres and Tuvok are captured by the Mokra during an away mission to find tellurium. She is then assisted by a man who thinks she is his daughter.

Chakotay feels responsible after Seska masterminds a successful raid on the Voyager that gives the Kazons vital Federation technology.

Voyager encounters people of Kes's race, the Ocompa, living on a space station; they lead the crew to the female of the Caretaker's species, who believes they caused the Caretaker's death.

On an away team looking for needed resources, Chakotay is reminded of his youth when he disappointed his father by not embracing his tribe's cultural heritage. He finds a familiar cultural symbol drawn in the ground used by his ancestors to "heal the land." Chakotay then tries to contact the beings his tribe calls the "Sky Spirits." Meanwhile, the Doctor continues to monitor Ensign Samantha Wildman's pregnancy.

A strange force causes the crew to enter a delusional state in which their most buried thoughts come to the surface.

During a shuttle mission to replenish Voyager's food supplies, Neelix and Lt. Paris discover an embryonic pod and become caretakers of the hatchling infant.

While giving a party for Kes, the crew starts encountering a spatial distortion phenomenon. It gradually starts occurring inside the ship, changing Voyager's structural layout.

Stardate: 49011. Ensign Harry Kim arises one morning to find he is back in San Francisco on Earth with his girlfriend, Libby. In this alternate reality, Starfleet records show he never served aboard Voyager, which Starfleet considers lost. Instead, Kim works in Starship Design at Starfleet Headquarters. To help him restore reality, he enlists the help of a shady figure in France named Tom Paris, who has no idea who Harry is.

When Voyager's crew encounters a swarm of strange alien lifeforms in space, the aliens start forming what seems to be a attachment to Voyager. Meanwhile the encounter seems to accelerate Kes's reproductive cycle that comes only once in her species lifetime.

The ship's holographic doctor has a strange encounter with Lt. Barclay that leads to him having problems telling reality from fiction. He is lead to believe that Voyager is nothing but a holographic simulation that he must fix.

Stardate: 49005.3 While performing a ritual to honor the anniversary of his father's death, Chakotay's shuttlecraft unknowingly violates Kazon-Ogla space. He becomes the target of Kar, a young Kazon boy undergoing a manhood ritual to earn his warrior name and place among his people.

The crew of Voyager discovers an unusual object floating in space while following a particle trail. They then land on a planet and discover an old Earth aircraft and then are led to a cave that contains cryogenic units with people from Earth in them.