Stardate: 48975.1 Voyager comes upon, to their surprise, a vintage 1936 pickup truck floating in space. To add to the mystery, the truck's radio is receiving a distress signal, which Voyager tracks down to the source planet. The mystery deepens even more when they find people from Earth in frozen animation there.
The crew learns the planet is also inhabited by human descendents of the frozen humans. The crew must decide if they want to stay on this lone Earth-like planet, or continue on the journey back to the Alpha quadrant. Will Janeway have enough crew left, after their decisions are made, to continue Voyager's trip home?
Stardate: 49005.3 While alone aboard a shuttlecraft remembering the anniversary of his father's death, Chatokay is captured and becomes caught up in a Kazon right of passage ritual. Unfortunately, the killing of Chakotay is a the prime part of this ritual. Can Voyager rescue him in time? Or can Chakotay rescue himself?
Stardate: 48892.1 When the Doctor is activated, he learns the Janeway has been injured, the crew has abandoned ship, and the Kazon are on board the ship. Only Janeway, Torres, and Neelix have remained on board.
Things turn even more strange when Reginald Barclay appears and tells the Doctor that this is just a computer glitch; he is on Jupiter Station, and there is no starship Voyager lost in the Delta Quadrant. Barclay tells the Doctor he must destroy the computer-generated Voyager to repair the glitch.
Stardate: 48921.3 Voyager is trapped by an encounter with space-born life forms, whose presence leads to strange effects on Kes. One effect is to push Kes into early Elogium, or the one period of time in their lives when Ocampans can give birth.
While Neelix considers the possibilities of fatherhood, Voyager must deal with a larger member of the life forms, which views the ship as competition for its mates.
Stardate: 49011 Waking up, Ensign Harry Kim realizes that something is wrong when he sees his girlfriend by his side and the cityscape of San Francisco outside his apartment window. Somehow, he has been removed from Voyager and sent to another place in time. Accessing classified files on the Voyager in this new time and place, he learns that a friend from the ship is also on Earth. Wishing to return to his post, Kim seeks out Tom Paris.
Stardate: Unknown Voyager encounters a spatial anomaly that disables Voyager's warp drive and communications. What's worse, the ship itself has become distorted, with passages and turbo-lifts going to the wrong locations; the crew can't get to where they need to go. The distortion of Voyager is compounded by the fact it is will soon encompass the entire ship. The crew tries desperately to stop the anomaly's advancement before the ship is destroyed.
Stardate: 49068.5 After Paris becomes attracted to Kes, and Neelix notices, tempers flair. At the same time, Voyager takes a detour to a M-Class planet that could have enough vegetation to supplant the ship's dwindling emergency rations. However, transporters will not work on the planet, so a shuttlecraft will have to be taken. Being the best pilot aboard and the resident expert on food in the Delta Quadrant, Paris and Neelix are assigned by Janeway to travel down together. On the way down, things go awry and Paris and Neelix must rely on each other to survive.
Stardate: Unknown Entering a possible dangerous area of space because of the Bothan race who control it, Captain Janeway begins to succumb to exhaustion. On the Doctor's orders, she takes some time off to play out more of her holosuite novel. Upon exiting and handling a first contact meeting with a Bothan, she begins to see the characters in her program around the ship.
Stardate: Unknown On an away mission to what appears to be an uninhabited planet, Chakotay finds the people his ancestors knew as the "Sky Spirits". This leads to Chakotay having flash backs to his conflicted youth and his relationship with his father. Tuvok and Torres successfully beam back to Voyager, but Chakotay can't be found. The crew has to fight the strange storms and elements of the planet in order to rescue Chakotay.
Voyager discovers energy reading believed to be emanating from the female Caretaker who had been the companion of the male Caretaker that brought Voyager to the Delta Quadrant ("Caretaker"). The remains of the male Caretaker act as a beacon and lead Voyager to a space station with a group of psychically advanced Ocampa being protected by the female Caretaker, named Suspiria.
The Kazon lead Voyager into a trap and are able to steal a Federation transporter module. Janeway tells the Kazon the module is useless to them without Federation knowledge on how to use it. The crew is then shocked to learn that Seska is now part of the Kazon crew, and has the knowledge to put the module to the Kazon's use.
Voyager, in desperate need of Tellerium, which will provide a stabilizer for their warp core, causes Janeway and an away team to beam down to a planet that has a supply of this substance. However, the city they beam to has an occupying force known as the Mokra. Tuvok and Torres are then captured by the Mokra, Neelix escapes back to Voyager with the needed Tellerium, and Janeway escapes only to find a mentally unstable ally, who believes Janeway is his missing daughter.
Now Voyager, with Janeway on the planet with a mentally unstable suspect, must find a way to rescue their fellow crewmen from thier secure prison facility.
Stardate: Unknown Voyager finds and beams aboard a deactivated humanoid robot floating in space. Torres is intrigued, and tries to reactivate it, with alarming results.
Stardate: 49337.4 Janeway takes Chakotay's advice and tries to form an alliance with one or more Kazon factions, in order to smooth their way through the system. Neelix gets captured in the process, but then meets one of the leaders of the Trabe. The Trabe had once enslaved the Kazon, but now they fight the Kazon for their survival.
Janeway seeks the Trabe's help in forming her alliance with some of the Kazon factions. However, the Trabe appear to have their own agenda.
Stardate: 49373.4 Voyager's crew work on designing a small vessel capable of going Warp 10, or being everywhere in space at the same instant. Paris takes the vessel out for a test flight, and everything appears to have gone okay, until Paris later collapses in the mess hall. The Doctor finds Paris' body is mutating, but he can't find any way to stop it.
Stardate: Unknown While trying to find a problem with one of Voyager's systems, the crew stumble upon a dead body in a conduit in Engineering. Tuvok's investigation leads him to a Betazoid who was once a Maquis. Trying to gather all the evidence, Tuvok mind melds with the suspect; the results of which proves to be very disturbing to all.
Stardate: 49447 Voyager encounters the debris field of a destroyed ship. Evidence points to a Cardassian drone, a weapon of mass destruction, that was taken over by Torres to work for the Maquis and destroy a Cardassian fuel depot while she was still in the Alpha Quadrant. Somehow, the drone has been tossed into the Delta Quadrant where, now working with a faulty computer system, it has resumed its search for the Cardassian target that is now over 70,000 light years away.
Stardate: 49301.2 While trying to take in a sample of a rogue comet, the crew of Voyager inadvertently beams aboard a member of the Q, who has been imprisoned in the comet by the Continuum due to his desire to commit suicide. When the Q who had pestered Captain Jean-Luc Picard for so many years materializes, Q asks for asylum on Voyager, which leads to a lengthy court hearing on this request.
Stardate: 49504.3 Voyager answers the distress signal of a Vidiian ship and transports the lone occupant to sickbay. The occupant is suffering from the Phage, and near death. The Doctor puts the unconscious patient into a coma, but then he links her brain's synaptic activities to a holodeck created virtual rendition of the Vidiian without the disease. When she wakes, the Vidiian gazes upon a healthy face she had not seen since she was seven years old. However, the holo-image will only keep her alive for a short period of time. The Vidiian, a hemotologist, and the Doctor work together to restore her synaptic functions to her old body before her brain waves disappear and she dies.
Stardate: 49485.2 Starting his one morale booster series aboard Voyager, Neelix begins his foray into journalism. One of his first assignments begins when he learns from a Talaxian friend that a Talaxian freighter is set to rendezvous with Voyager to pick up a passenger. Neelix investigation leads to a meeting with Captain Janeway and Lieutenant Tuvok, who inform Neelix that a disgruntled Tom Paris is leaving the ship.
Stardate: 49548.7 Voyager attempts to avoid a Vidiian attack by entering a plasma cloud. Upon leaving the plasma cloud, strange and disturbing events occur among the crew, related to their time in the cloud.
After Tuvok crashes his shuttle onto a planet, he discovers he is not alone. Several children appear to have been abandoned there by their society. Tuvok must solve the reason the kids have been abandoned, and get the shuttle working again.
Upon responding to an automated beacon message, the crew finds stasis pods, some of which still have living inhabitants. Several, though, have dead bodies. The cause of their deaths appears to have being scared to death.
The crew also finds that the live bodies in the stasis tubes are interacting with each other. The crew decides to uses an available tube to interact with the survivors. What they find shocks them, and puts the rescuers' lives in danger.
A transporter accident combines Neelix and Tuvok into one person. This new person wants to be called "Tuvix". The crew feverishly works to find a solution to this situation; but does Tuvix want to be changed back? And, does Tuvix have the right to decide the fate of Neelix and Tuvok?
While on an away mission, Janeway and Chakotay are bitten and become infected with a disease that the doctor can't cure. Something about the planet prevents the infection from killing the two, but they are force to remain there if they are to survive. Voyager is forced to continue their trip home without the them.
Chakotay receives an urgent subspace message from Seska. She tells him that Culluh plans to remove her and Chakotay's new born child from her. Chakotay is conflicted as to what he should do. Should he ask the crew to fly into harms way to save his son? Should he even trust Seska to be telling the truth?
Things take a sudden turn when one of Culluh's crew shows up and tells them that Cullah has killed Seska, and has taken the baby to a certain world to be raised. As Voyager heads off to rescue the baby, they find they are under constant attacks by the Kazon.
Just when things begin going their way, the Kazon spring their own surprise on Voyager. The Kazon now have the upper hand.