Janeway and most of the crew, abandoned with none of their technology on the volcanic planet by the Kazon Nistrim, struggle to survive against both the elements and a group of primitive cave-dwellers. Aboard the captured Voyager, the Doctor and recovering sociopath Lon Suder form an alliance to try to wrest control back from Cullah's boarding party while Tom Paris seeks help from a distant group of Talaxians. Suder makes the greatest sacrifice of all as he finds he must release the dark side of his psyche in order to save the ship. Chakotay establishes the rudiments of communication with the tribesmen on the planet. And Paris convinces a reluctant Commander Paxim to use his Talaxian fleet in an attack which depends on timing to avoid disaster.
With the crew excited at the prospect of a new source of sirillium, Voyager approaches a Class 17 nebula gaseous anomaly, but at the sight of it on the viewscreen Tuvok experiences a flashback to what is apparently a traumatic experience in his youth. Yet it is not an episode from Tuvok's past and the Doctor has no explanation, except for the observation that Tuvok's neural synapses break down each time the 'memory' returns. When Tuvok begins to express concern over finding cloaked Klingon ships 'this close to Klingon space', he decides to regress using the technique of the Vulcan mind meld, asking Janeway to be his guide and counselor. She joins in his memory as an outside observer to objectify the experience. Yet he does not return to the memory in question but to a memory of his first deep-space assignment, 80 years previously aboard the Excelsior. It is here that the source of the mystery lies, but they are fighting time as Tuvok's neural synapses continue to degrade and Janeway suddenly becomes a participant in Tuvok's memory and not just an observer.
Harry Kim, disoriented and injured, finds himself in a circle of brutal thugs, his new neighbors in an alien prison camp. Harry finds help in the form of fellow prisoner Tom Paris, and they begin trying to escape, but their efforts are hindered by rising tempers, caused by implants that stimulate random, violent impulses. Janeway receives word that Kim and Paris have been convicted of a terrorist bombing on a planet they were visiting, and that the sentence - lifetime imprisonment in an inpenetrable location - has already been carried out. Paris and Kim find that the only escape possible from their prison is through a chute that is protected by a lethal force field, but during an attempt to short out the chute's defenses they are attacked and Tom suffers a severe stab wound. The Voyager crew track down the real terrorists, but by the time Janeway can win a confession and clear her crewmates' names, their cellmates may have murdered them - or they may have killed each other.
En route back to Voyager, the shuttle carrying Paris and Torres is boarded by two unfamiliar alien lifeforms, who render the Voyager crewmembers unconscious and then leave. Voyager recovers the shuttle, but as the Doctor treats the badly injured Paris, he suffers from an increasing memory loss that he first encountered while running an opera program on the holodeck. Kes notices the Doctor's forgetfulness and alerts Torres to the problem. One easy solution would be to completely reinitialize the Doctor, but he would lose every memory of the past two years. In the meantime, Janeway's decision to stealthily pass through the territory claimed by a hive of insectoid beings may result in Voyager being destroyed by the aliens' sheer numbers.
The investigation of a possible wormhole reveals signs of visitors from the Alpha Quadrant on a primitive planet. Chakotay and Paris make an incognito visit to a location where sensors have detected a replicator in use, only to find a village of humanoids who seem obsessed with charging money for any goods or services, no matter how insignificant. At the heart of this culture lie two Ferengi, stranded in the Delta Quadrant since they were trapped by the Barzan Wormhole discovered by the Enterprise seven years earlier. The Ferengi have come to this society as gods bearing wisdom but their true motive is to exploit the native population for their own gain. Janeway sets a plan into motion which involves Neelix masquerading as an envoy from the Grand Nagus. But if his disguise fails to fool the Ferengi, he may find that these profit-mongerers will do anything to keep their grasp on godhood.
As Voyager ferries some telepathic Delta Quadrant denizens from a colony to their home world, B'elanna experiences an intense dream about a member of their race, even though the object of her fascination is not one of Voyager's passengers. B'elanna's dreams take stranger turns as they progress along a continuing path, telling her a specific story from the past, from point of view of one of the passengers. Though allegations of telepathic interference are denied, B'elanna finally encounters the person whose memories have been transmitted to her - an elderly woman who dies immediately after sending B'elanna the last of her experiences involving a rebel faction of the aliens' population which was massacred for opposing the government.
On a visit to a monastery on an alien world, Kes and Neelix visit a shrine. When Kes approaches it, an energy field knocks her out, and a government official informs the crew that Kes has been punished by the world's ancient spirits for trespassing on holy ground. Beamed to Voyager's sickbay, Kes is slowly dying and the Doctor can offer no alternatives to save her. Janeway beams down to the planet to undergo any voyage of discovery necessary to save Kes, but her path is less than straightforward and may not yield any useful information.
A brief encounter with a vessel whose lone occupant claims to be a Federation time scout from 500 years in the future results in a fierce firefight. The future captain describes a cataclysmic disaster in the 29th century resulting from an incident that Voyager is about to initiate. The timeship is damaged in the ensuing battle and falls back into the temporal rift through which it arrived, which also drags Voyager in. Voyager is taken back to Earth, 1996, and faint signs are detected of the timeship. Janeway, Chakotay, Paris and Tuvok beam down incognito to search for the wayward vessel, but unknown to them their own ship has been detected in orbit by an astronomy graduate named Rain Robinson. Rain contacts computer magnate Henry Starling, who is in possession of the timeship while its original occupant languishes on the streets of Los Angeles. Tom and Tuvok make their way to Griffith Observatory to erase Rain's evidence of Voyager's presence, but she catches them in the act and is hot on their trail as one of Starling's employees attempts to kill them all.
Tuvok and Paris enlist Rain's help in contacting Voyager and setting a trap for Starling which involves pinpointing his location to allow a transporter kidnap from a shuttlecraft. Starling, however, has two tricks up his sleeve - the Doctor, equipped with a portable holo-emitted, is his hostage, and he has a device to thwart the shuttle's transporter. The shuttle's systems overload and the shuttle, piloted by Chakotay and Torres, crashes in the Arizona desert, but the Doctor escapes as Voyager takes over transport of Starling. Chakotay and B'elanna fall into the hands of a cult militia group, but are rescued by Tuvok and the newly independent Doctor. Starling escapes and launches the timeship despite Janeway's warnings, but his scheme for Earth's future won't exactly unfold as planned.
Voyager's crew barely manages to rescue three occupants of a battle-damaged spacecraft, one of whom dies in sickbay immediately after transport. When Voyager returns the survivors to their planet, an official beams aboard and is killed by Kes, who also kills the transporter chief and struggles with Janeway. Kes and the other refugees steal a shuttlecraft and run for it. Kes' body has been taken over by Tieran, a power-mad dictator who has developed the ability to transfer his consciousness into the minds of others to insure his immortality. Tieran kills the rightful ruler of his people and assumes power, trying to coerce the youngest heir into backing his coup. The elder heir, Demis, has beamed aboard Voyager to coordinate efforts to restore the original government, and despite his overtures of war, Janeway still insists on trying to recover Kes in body and spirit. Kes also intends to break free of Tieran's influence, but he proves to be a formidable enemy.
After the crew witnesses a supernova explosion from a safe distance, Janeway retires for the evening, only to be wooed in her quarters by Q, who claims to want to mate with her. Naturally, Janeway rebuffs Q's every advance, and eventually a female member of the Q Continuum appears, claiming that she is bonded to Q. As an argument ensues between the Qs, more imminent supernovae are detected and Janeway orders the ship clear of the destruction, but with so many stars exploding, Voyager can't avoid all of the shockwaves. Just before the first wave hits the ship, Q whisks Janeway into a representation of the Q Continuum in the context of the American Civil War. Q explains that the Continuum is in the throes of its own civil war, sparked by the death of a fellow Q he prosecuted on charges that a Q suicide would imbalance their whole society. Q's desire to mate with Janeway is the result of his belief that, from his past experiences with Janeway and Picard, a hybrid child would introduce the omnipotent Q to the nobility of humans.
Janeway and Neelix return from a diplomatic mission to find Voyager adrift and the crew unconscious, concentrated in a few areas of the ship. They find evidence of alien lifeforms that can punch their way through doors and equipment, and a chance encounter with one of the aliens results in Neelix's disappearance. Janeway arms herself as she tries to find out what has happened to her crew, and encounters and kills another of the alien lifeforms, but not before she has been infected by an insect-like airborne virus. She makes her way to sickbay and the Doctor describes an ill-fated humanitarian mission that resulted in the infection of the entire Voyager crew. The virus breeds as a microscopic organism and grows to its insect-like size to leave its victims' bodies, finally evolving into a monster-sized attacker that seeks out new prey. Janeway must find a way to single-handedly rid Voyager of a scourge that outnumbers her by a factor of billions to one.
With Neelix pursuing a promotion, Voyager stops at a trading port at the edge of the vast and uncharted Nekrit Expanse. Although the ship's environmental control systems require Pergium for replenishment, it seems to be unavailable until an old friend of Neelix turns up with a plan to obtain some. But when this plan turns out to involve dealing narcotics in dark passageways late at night, things begin to get out of control.
The crew begins an analysis of an unusual phenomenon called an inversion nebula which might provide fresh insight into the nature of plasma reactions. Harry falls in love with a holodeck character and when Tuvok attempts to help him use Vulcan mind-control techniques to overcome his infatuation with a computer-generated subroutine, the crew discovers that the object of Harry's desires is actually an alien life form which has used the holodeck to interact with the crew. But Tuvok's attempts to help set off a cascade of jealousy which endanger the entire ship.
While on a planetary mission, the captain and Chakotay crash and are killed by the Vidiians. Suddenly they are back aboard the shuttle approaching the planet where they recognize the sense of deja-vu. This time they recognize a Vidiian ship and attempt to outrun it, but fail and loop back to the beginning of the sequence again. Now they make it back to the ship, but Chakotay has no memory of the time loop. Janeway has the Doctor examine her and is shocked to learn that she's been infected with the Vidiian phage.
Large deposits of gallicite draw Voyager to an abandoned planet for this material will enable a refit of the warp coils. But while preparing for the expedition, Ensign Vorick comes under the influence of the Pon Farr and declares his intention to take B'ellana as a mate, attempting to force his affections on her. Although this results in a dislocated jaw for Vorick, the physical contact seems to have caused a change in the chief engineer resulting from a mating bond. As the odd triangle (which includes Tom Paris) is resolved, the crew discovers that the planet is not abandoned after all, but is inhabited by the Sakari, a race which has developed camouflage to a high art to avoid their ancient enemies - the Borg.
While exploring the Nekrit Expanse in a shuttle, Chakotay responds to a distress call which recognizes their Federation signature, but when he goes to the surface to investigate he runs into a firefight between rival factions. Meanwhile, Voyager runs into an abandoned Borg cube adrift in space. It turns out that the people on the planet were once a part of the Borg collective, but the link was severed about five years previously and they fell into anarchy. A small group of the castaways tries to enlist Chakotay's help to bring some order to the society, but the Voyager crew is concerned that this action would re-awaken the Borg ship.
The Doctor attempts to modify himself by adding behavioral subroutines while the Voyager crew treats with the Mikhal Travelers, trading supplies for information on the Nekrit Expanse. But while the Travelers seem very helpful, and Kes becomes romantically involved with one of their pilots, a strange series of changes begins to take place in the Doctor. The new subroutines seem to have created an alter ego which is becoming separate from the Doctor's normal personality. He begins to display a violent jealousy over Kes' blossoming relationship, combined with the ruthlessness to carry out his intentions. B'ellana's efforts to help modify his program only brings the ship, crew, and especially Kes closer to danger.
Neelix joins a crew attempting to help Nezu colonists during a series of asteroid collisions. Voyager fails in its attempt to vaporize an incoming asteroid and discovers that they're artificially guided. When Neelix and Tuvok are abandoned on the planet just before the next scheduled asteroid strike, they and some colonists use a maglift carriage to climb an orbital tether to a point where they can contact the ship. But one of the Nezu is determined to keep the others from passing on what they know. As the carriage rises into the thinning atmosphere, they discover what the real motivation behind both the asteroids and the surrounding secrecy is.
Ensign Kim fires without warning or explanation on an alien ship. This startling action has apparently saved Voyager, but Harry continues to 'remember' things about a place he's never been. When more Nasari ships appear to press the attack, Voyager is saved by a Taresian vessel and escorted to their homeworld with the surprising news that Harry is actually a Taresian - conceived in the Delta Quadrant and taken to Earth for fosterage unknown to his human parents. The Taresians bend over backwards to welcome Harry back to the fold, even preparing him for their form of multiple marriage, but Harry and the crew sense something amiss.
'Grandma Kes' awakens surrounded by people who claim they are her family, but whom she doesn't recognize. She fades into unconsciousness and reawakens at a slightly earlier time in her life. Although she remembers the experience, it apparently hasn't happened yet for the rest of the crew. Confused and frightened, Kes continues to experience the morilogium - the final phase of the Ocampan lifespan - as well as the temporal effects of life-extension treatments in the Doctor's experimental bio-temporal chamber. As the temporal effects grow more and more out of control, Kes regresses through her entire life, seeing a 9-year history of Voyager in reverse as she struggles to understand her situation and how to stop what is happening to her.
As the crew investigate the apparent destruction of a Vostigye science station, the Doctor works on a program which has created a family for him to interact with. He invites B'elanna and Kes to join him in the holodeck for dinner with his new wife and children, and they strike the chief engineer as being 'ridiculously perfect'. B'elanna offers to help tweak the program a bit to bring it more in line with the real experience of home life.
The Voyager crew are unwitting research subjects after scientists of the Voth race, saurians who believe they were the first intelligent beings to evolve in the Delta Quadrant, discover the human remains of Voyager crewman Hogan and find a genetic pattern similar to their own. When Gegen, the chief researcher, suggests that based on these findings, the true origin of the Voth is Earth, their leader, Minister Odala, deems him a heretic. To prove his theory, Gegen and his assistant Veer track down Voyager, infiltrate the ship and take their next research subject, Chakotay, hostage.
Chakotay startles B'elanna by recruiting her for a Maquis mutiny, and then proceeds to carry it out. Things get even stranger when Seska turns up as one of the mutineers. Suddenly Paris walks into the scene, revealing the fact that Torres is playing a holo-novel. The experience was designed by Tuvok as a training exercise shortly after the joining of the two crews when the security officer felt that a mutiny was a real possibility. The fresh literary material is so intriguing to the crew that many of them begin surreptitiously playing the program and Janeway instructs Tuvok to write an ending and make it more than a training exercise. But Seska had discovered the program before she defected to the Kazon and she rewrote the subroutines to take her revenge on Tuvok for having betrayed the Maquis back when they were still in the Alpha Quadrant.
As Nyrians begin appearing on the Voyager at 9:20 intervals, crewmembers begin to disappear at the same rate. Although the visitors seem peaceful, Janeway suspects an organized takeover. Her suspicions are confirmed as the crew find themselves in a holographically generated environment where they are held prisoner. The startling appearance of a fellow prisoner from an adjoining 'cell' makes them realize how to move between areas of what turns out to be a giant ship filled with different environments and a command center with an extremely long-range transporter.
As Voyager approaches the edge of Borg space, they discover a narrow passage which is empty of Borg activity and decide to try to thread their way through it in an effort to avoid confrontation. But they suddenly realize that the reason for the lack of Borg activity is the invasion of another species which apparently has no trouble at all defeating the Borg cubes with bio-ships impervious to assimilation. A Voyager away team visits a dying cube ship which has one of the alien vessels attached to it. The crew manage to download the Borg's information on the new species, named '8472', but Harry Kim is attacked by the pilot of the bio-ship and is given a virulent infection which begins to devour him from the inside out. While Ensign Kim fights for his life, a conflicted Janeway grapples with the decision of either guiding her crew through the dangerous Borg territory which is lined with a new mortal enemy or turning around and ending all hope of ever getting home.