Stranded by the Kazon on the planet Hanon IV, the crew of the U.S.S. Voyager is forced to defend against the planet’s primitive inhabitants. Following the death of a crew member by an unknown creature in nearby caves, and the disappearance of Kes and Neelix, the crew are forced to fashion primitive weapons in order to survive.Meanwhile, Maje Culluh is in command of the Starship Voyager, and plots to attack other Kazon sects with ‘his’ new ship. The only chance for regaining the vessel weighs upon Ensign Suder and the holographic doctor — the last of the crew still on the starship.
Tuvok suddenly begins having strange, disorienting attacks which cause a disturbing childhood memory to resurface. As the trauma begins to degrade his neural system he knows he must take action or he will die. To access and conquer the debilitating memory fragment, he asks Captain Janeway to act as his guide and enter into a mind-meld with him. Amazingly, the mind-meld takes Tuvok and Janeway to the scene of the young Vulcans first Starfleet duty – on the bridge of the U.S.S. Excelsior with Captain Hikaru Sulu in command.The Doctor and Kes monitor them, Janeway and Tuvok delve deep into the mind-meld. Tuvok attends to duties with his fellow crew members including Commander Janice Rand, while Janeway in anunseen observer. She learns that Tuvok’s first deep space assignment, as a junior officer aboard the U.S.S. Excelsior, was a disagreeable tour of duty for the young Vulcan and sees how it eventually led to his departure from Starfleet over 50 years ago. Janeway also has a chance to see firsthand what her kindred officer, Captain Sulu, choose to do in the heat of battle with the Klingons, led by Commander Kang.Tuvok clashes with Sulu over the Captain’s orders to make the bold mission to the Klingon Homeworld to rescue Captain Kirk and Doctor McCoy and Janeway gets to “ride shotgun” with a different breed of Starfleet officer. Janeway and Tuvok continue with the mind-meld in hopes that it will yield just what repressed memory is causing such a physical reaction in Tuvok – until something goes wrong and without warning, Sulu and the U.S.S. Excelsior crew can see Janeway.
While on an Akritirian planet, Paris and Kim are believed to be members of the Open Sky terrorist group and are arrested, tried and convicted of planting a trilithium-based bomb. Before they know it, they are piled into a dark, impenetrable prison at the end of a mysterious chute. Kim tries to devise an escape and protect a severely injured Paris who has been stabbed by a ranting prisoner. But they realize that, like each crazed inmate, they are fitted with a clamp which causes each man to slowly kill one another. Meanwhile, Janeway tries to prove their innocence.Under brutal attack from the Akrititians, the U.S.S. Voyager crew detects another source of trilithium in the system, a ship piloted by Piri and Vel, a sister and brother who are purported members of the Open Sky. They transport them aboard and are prepared to turn them over in exchange for their innocent crew members, but the Akritirian leader Liria, refuses to surrender Paris and Kim. In a bold move, Janeway asks Neelix to bring his ship out of storage for a special mission.
The Voyager crew picks up passengers from the homeworld Enara Prime and learns of their telepathic ability. Before long, Lieutenant Torres begins having intense, sensuous dreams of herself as a young girl involved in a forbidden romance with Dathan, a member of the Regressives, a subgroup which once resisted Enaran technology. The dreams turn haunting for Torres as the young girl’s father Jareth, participates in a resettlement of the Regressives — and eventually their total extermination. Strongly affected by the horrible visions, Torres realizes that the Enarans have concealed a part of their history from their descendants and that one of them aboard Voyager doesn’t want her buried memories to die.
Kes is left for dead after she enters a sacred shrine on the Nechani homeworld and is hit by a mysterious energy burst. The Nechani explain to Janeway that monks receive purification of their souls in the shrine and the spirits have punished Kes for trespassing. While Neelix researches the shrine and the ritual the monks undergo there, Janeway undergoes the arduous rite of passage herself. Although she is certain there’s a scientific reason for the energy burst, she hopes to beg to the mercy of the “spirits” and save Kes.
The Doctor’s rehearsal of an opera duet on the Holodeck is interrupted when he is called to treat the severely injured Lieutenant Paris who, while aboard a shuttlecraft with Torres, has been attacked by an unknown alien force. When The Doctor cannot remember the medical procedures necessary to save Paris, it is discovered that the Emergency Medical Holograph database has overloaded and The Doctor’s memory circuits are rapidly degrading.While the rest of the crew fends off the cluster of alien ships — the first they have ever encountered with transporter technology in Delta Quadrant – Torres attempts to reinitialize The Doctor’s program, but forewarns that her efforts would restore the original E.M.H program, causing The Doctor to in effect, be erased.As the rapidly failing Doctor becomes more and more disoriented, Kes pleads for an alternative remedy. So Torres leads The Doctor to the Holodeck where the enter Jupiter Station, the place where his database was originally written, and find that the diagnostic matrix is a holographic recreation of his creator, Dr. Lewis Zimmerman.
When the U.S.S. Voyager detects replicator technology and Alpha Quadrant inhabitants on a nearby planet, Chakotay and Paris transport there to find an impoverished, struggling society. They soon find a palatial temple and two Ferengi — Arridor and Kol — decked out in silk and gold jewels who are passing themselves off as demigods to the people there. It’s up to Chakotay and Paris — with the help of Neelix — to thwart them.
Captain Braxton of the 29th century Timeship Aeon hails Janeway and the crew to inform them that the U.S.S. Voyager is responsible for a catastrophe in his century and he’s come back in time to prevent that occurrence by destroying them. The U.S.S. Voyager crew is forced to engage him and, although equipped with only 24th century technology, they’re able to partially disable his weapons. Suddenly, the U.S.S. Voyager is pulled into a spatial rift which transverses them across the galaxy to the Alpha Quadrant. They are stunned to find they’re back home above Earth, only in the wrong time — the 20th century.
While the U.S.S. Voyager orbits above North America with its weapons and long range sensors disabled, Tuvok and Paris are missing in Los Angeles and must enlist the help of young astronomer Rain Robinson and use cellular telephone technology to communicate with their crew. Meanwhile, corrupt computer magnate Henry Starling accesses the U.S.S. Voyager’s computer system and downloads The Doctor’s program, holds him hostage and reconfigures him with 29th century technology.In an effort to conceal themselves while trying to stop Starling, Chakotay and Torres set out in a shuttlecraft but crash land and are captured by a militia group in Arizona. Then, as Starling prepares to launch the timeship, the city’s news organizations report the sighting of another mysterious flying object — U.S.S. Voyager.
As The Doctor and Kes treat three injured aliens whose ship was detected adrift in space, one of them — an egomaniacal political extremist named Tieran — dies but not before he transfers his own mind to the body of Kes, controlling her and accessing her own Ocampan powers. Then, Kes/Tieran, launches a shuttlecraft and makes a coup attempt on his home planet of Ilari.
While the Voyager crew witnesses several rare supernova explosions, Q arrives in the Captain’s quarters to implore the outraged Janeway to conceive his child. Citing his loneliness and need for stability, Q offers that their offspring would combine the omnipotent power of his species with the feelings and emotions of the human race. Q is daunted and continues his pursuit of the uninterested Janeway just as a jealous female Q pops up to bring Q back to the Continuum.While Voyager is deluged by shock waves from the supernovas, Q escapes to the Continuum with Janeway in tow, leaving the female Q bereft of her unlimited powers aboard a stranded Voyager. There, Janeway discovers the true reason Q is desperate to procreate — for the continuation of the Q race.As a result of Q’s work, the Q Continuum is colorfully represented forJaneway as the ante-bellum south, circa 1861. The Starfleet Captain finds herself dressed as a southern belle, fortified inside an elegant manor house amidst the Continuum’s civil war. Not only does Janeway see that Q can be physically injured, she realizes that mating among the Q is unprecedented and that the fulfillment of Q’s plan — to have a baby — is the only way to avert the destruction of the Continuum.
The U.S.S. Voyager is seized by a macrovirus alien — an unknown gelatinous lifeform which attacks and overwhelms the crew and disables the ship — and Captain Janeway must face the fight of her life, crawling through the disabled ship’s dark passageways to elude the alien’s assault. Meanwhile, The Doctor goes on his first away mission to the Garan mining colony to locate the source of this mysterious and severe viral infection.
When the U.S.S. Voyager crew transports to the heavily secured space station to trade for supplies, Neelix meets up with Wixiban, an old Talaxian acquaintance who dupes him into using Federation shuttlecraft to traffic narcotic substances. When Wixiban murders one of his drug buyers, Paris and Chakotay are implicated while a guilt-riden Neelix returns to the ship.
Disturbed by the fact that he’s falling in love with Marayna, a Holodeck character, Ensign Kim begs Tuvok to teach him how Vulcans to suppress their emotions. When Tuvok intervenes, Marayna befriends and tries to seduce him, too. A jealous Kim is infuriated with Tuvok but then Marayna reveals her true intentions.
During their exploration of a decimated colony, the Voyager Away Team is thrown into turmoil with the sudden onset of the Vulcan mating season. The ensuing, irrational advances of a Vulcan crew member wreak havoc when they trigger Lieutenant Torres’ involuntary Klingon mating instincts. Meanwhile, Commander Chakotay spots the remains of one of the colony’s invaders – The Borg.
After her shuttlecraft crash lands, a critically injured Captain Janeway is attacked by Vidiians and has a mysterious near death experience during which she encounters her father, Admiral Janeway.
In response to a distress signal, Commander Chakotay lands his shuttlecraft on a planet’s surface but is viciously attacked. He’s swiftly rescued by a colony of formerly assimilated Borg and goes to extreme measures when he allows their resident physician, Dr. Riley Frazier, to heal his neural injuries by linking him to a remnant of the Borg Collective consciousness.Meanwhile, after Janeway and her crew find a suspicious Borg ship disabled and adrift in space with a thousand members of the powerful Borg race lying dead aboard it, they transport one of the corpses to Sickbay so the Doctor and Kes can perform an autopsy.
When a Nezu planet is bombarded by asteroids and its inhabitants are facing evacuation, Voyager intervenes by sending Tuvok and Neelix to join several prominent members of the Nezu on a rescue mission. Soon it is learned that there’s a traitor in their midst, and Tuvok’s condescending attitude pushes Neelix to the breaking point.
To improve his performance as the ship’s physician, The Doctor undertakes a personality enhancement project on the Holodeck, incorporating several accomplished historical figure’s traits and temperaments into his Starfleet database. But he also adopts several aberrant character traits from those non-fictional figures and is soon over taken by a dangerous, cruel Mister Hyde-like personality.Meanwhile, the U.S.S. Voyager hosts the Mikhal Travelers, a race of explorers with extensive knowledge of the territory. As Kes spends time with one of them, Zahir, she’s overwhelmed with feelings that, having lived one third of her life, she’s reached a crossroads and asks permission to leave the ship.
Ensign Kim instinctively leads the ship to the mysterious Taresian homeworld where a shocking story of his birth is told by members of the almost exclusively female population — he’s part alien — and they want him for reproductive purposes.
When Kes undergoes treatment in a bio-temporal chamber to extend her lifespan, her cells are left in a state of flux causing her to be out of temporal sync. She then travels back and forth through time, experiencing the beginning and final phases of her Ocampan lifespan and gets a glimpse of the U.S.S. Voyager crew’s future.
After The Doctor creates a holographic wife and two children for himself in order to enhance his performance as a caring physician, Torres modifies the program to make The Doctor’s picture perfect Holo-family more of an authentic experience. Soon, his teenage son is listening to Klingon music and The Doctor deduces that he has more than he has bargained for.
The U.S.S. Voyager crew are unwitting research subjects after scientists of the Voth race, saurian-like aliens who believe they were the first intelligent beings to evolve in the Delta Quadrant, discover the human remains of a U.S.S. Voyager crewman (Lieutenant Hogan killed in the episode “Basics, Part I”) 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 the U.S.S. Voyager, infiltrate the ship and take their next research subject, Chakotay, hostage.
One by one, Janeway’s crew suddenly and mysteriously trades places with Mercurial aliens from Nyria Three. As Janeway quickly becomes surrounded by these seemingly perplexed strangers who react strongly to the ship’s temperature and lights, she must scramble to keep control of her ship. Meanwhile her confused crew is transplanted to an idyllic yet artificial world.
Suspicion and animosity run rampant when members of the crew discover a secret holographic novel program depicting Seska and the Marquis leading an insurrection aboard the U.S.S. Voyager. When crew members surreptitiously play the program, they are each cast into the role of a Starfleet security officer who is approached by Chakotay to help the Marquis with the mutiny.
As they approach the heart of dangerous Borg territory, the U.S.S. Voyager crew witness the near decimation of a Borg armada by a mysterious alien lifeform which is impervious to both Borg and Starfleet technology. When Kim and Chakotay lead an away team inside the heavily damaged Borg cube, they are able to investigate the alien lifeform’s bio-ship. Moments before they are transported out, Kim is viciously attacked by the mysterious organic looking alien. As he lies in Sickbay, contaminated with alien cells and transforming into an alien being, Kes has terrorizing premonitions about the new enemy and Janeway realizes it’s no longer the Borg they must be worried about.