The Voyager crew discovers several people who were abducted during 1937, including Amelia Earhart, cryogenically frozen on a distant planet.

Chakotay encounters a Kazon youth who is on an initiation rite: to earn his name by killing an enemy or be killed in the attempt.

The doctor tries to determine what is real and what is not when he is activated due to what appears to be a ship-wide emergency.

Space-dwelling life-forms cause Kes to enter the Ocampan fertile phase called Elogium, putting pressure on her relationship with Neelix when she wants to have his child.

Harry Kim wakes up in San Francisco having never been assigned to Voyager which Starfleet considers lost.

Voyager encounters an inversion field which twists and distorts the ship's hull. It rearranges the decks making it impossible for anyone to return to the bridge.

After a disagreement over Kes, Neelix and Tom Paris are trapped together on an alien planet and must work together to survive.

The Voyager crew enters a new region of space and begins to experience disturbing and violent hallucinations..

Finding a familiar cultural symbol on an away mission, Chakotay investigates the symbols and visions that are remarkably similar to one of his childhood experiences.

While attempting to make contact with the Caretaker's mate (who may have the ability to send Voyager home), the crew discovers a colony of Ocampa whose representative has an interest in Kes and helping her explore her telepathic powers.

While following a mysterious hail, Voyager is attacked by a Kazon-Nistrim ship. With the help of Seska, raiders steal a transporter module and escape. Embarrassed by the way Seska used him, Chakotay goes off alone to recover the Federation technology. As the Kazon sects gather for a final assault on Voyager, the crew makes a desperate attempt to rescue their first officer.

While buying tellerium on a planetary black market, a landing party is attacked by the Mokran police force. While Tuvok and Torres are taken into custody, Janeway is hidden by a member of the Alsurian resistance. Caylem is a tired old man who has been completely unstrung by the deaths of his wife and daughter in the struggle against the Mokra. In his sorrow, he believes that Janeway is his daughter and leads her into the heart of the Mokran defenses.

The crew beams aboard a damaged robot of humanoid design and B'Ellana takes up its repair as a challenge. When she manages to repair its power module, the robot asks her to produce more power modules so that more robots can be created. When Janeway objects, the robots kidnap Torres and threaten to destroy Voyager unless she cooperates. But the Praelor turn out not to be the only robots in the quadrant.

Under continuing attack from the Kazon, Voyager seeks an alliance. But when talks with the Kazon break down, Janeway opens talks with the Trabe, who are also trying to leave Kazon space. The Trabe once oppressed the Kazon, but they seem to embody Janeway's ideas of Federation principles and they propose a meeting among all parties - including the Kazon. The meeting goes well until a ship opens fire upon the participants, exposing a new threat and dissolving the peace process.

Torres, Kim, and Paris work as a team to cross the transwarp threshold and travel at warp 10, a theoretical impossibility which would allow the traveler to occupy all points in space simultaneously. Though the attempt is successful, Paris' biochemistry undergoes a massive change which causes him to mutate into a more evolved version of humanity. The new Paris kidnaps Janeway and they both cross the barrier in the shuttle, precipitating more changes in both of them.

When Crewman Darwin turns up dead all signs point to Crewman Suder, a former Maquis and a Betazoid, as the murderer. Tuvok mind-melds with him to better understand the roots of serial killing, losing control of himself in the process.

After coming upon a debris field, Torres realizes that it was caused by a powerful Cardassian weapon which had been brought to the Delta quadrant by the Caretaker. Due to the jump, its navigational system thinks that the Delta Quadrant's densely populated Rakosa 5 is its target instead of the Cardassian fuel depot on Aschelan 5 in the Alpha Quadrant. Unable to disarm the warhead, both Torres and Janeway face destruction as they try to save the planet.

When the crew investigates a strange comet, they accidentally beam aboard a renegade member of the Q continuum who had been imprisoned for wanting to die. When Q comes to take him back, the new Q requests asylum from Captain Janeway who convenes a hearing to determine whether asylum will be granted. Although Q attempts to influence the outcome, the Captain comes to a difficult decision on her own.

Voyager beams aboard a dying Vidiian woman. The Doctor creates an image of her from the transporter pattern buffer to stabilize her while he attempts a cure. She turns out to be a hematologist who was traveling to a distant colony to help combat the Phage. In curing her, the Doctor learns much about himself too.

We see the first episode of A Briefing With Neelix;, an internal broadcast which Neelix hopes will improve morale. But after speaking with Harry Kim, former editor of the StarFleet Academy newspaper, he is inspired to investigate the departure of Tom Paris. Tom's departure and his previous bad behavior were all a ruse to flush out the person who was passing information to Seska and the Kazon. But Neelix doesn't know this and jepordizes the whole scheme.

A schism duplicates everything in Voyager; except the antimatter, which both ships share. As they work together to resolve this problem, a Vidiian ships finds them.

Tuvok crashes on a moon were he finds a group of alien children who are disappearing, one by one.

The crew attempts to rescue three aliens in stasis from a bizarre computer program that is based on fear.

After a transporter malfunction, Tuvok and Neelix are merged into a single being. In the search for a way to restore them to their original forms, a moral dilemma is faced as the new being does not want to be terminated.

Voyager is forced to abandon Captain Janeway and Chakotay when they are infected with a terminal illness. Tuvok leads Voyager on a mission to find a cure.

Seska and the Kazon-Nistrim take control of Voyager and maroon its crew on a primitive planet.