Left for dead by the Kazon, Captain Janeway and her crew brave the elements and hostile natives on Hanon Four, a primitive planet. When one of their group is viciously killed and then Kes is abducted, Chakotay and Tuvok must attempt a precarious rescue. They prepare for a vengeful alien attack while a gloating Culluh, at the helm of Voyager, announces a new era in Kazon history and prepares to annihilate most of the Delta Quadrant.
As Culluh tests the ship's power, Seska activates the Emergency Medical Holographic Program only to have the Doctor report startling facts about her newborn baby. The Doctor detects that Ensign Suder is stowed away on board and learns that Lieutenant Paris, with the help of a Talaxian convoy, is piloting a damaged shuttlecraft, desperately working to somehow save Voyager. The Doctor soon arouses Seska's suspicions and is permanently deactivated, leaving Suder as the only hope to retake the ship. All the while, Suder is tortured by the realization that he must resort once again to violence.
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 Vulcan's first Starfleet duty - on the bridge of the U.S.S. Excelsior with Captain Hikaru Sulu in command.
While The Doctor and Kes monitor them, Janeway and Tuvok delve deep into the mind-meld. Tuvok attends to duties with his then fellow crew members including Commander Janice Rand, while Janeway is an unseen observer. She learns that Tuvok's first deep space assignment, as a junior science officer aboard the 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, chose 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 (Star Trek VI) and Janeway gets to "ride shotgun" with a different breed of Starflet officer. Janeway and Tuvok continue with the mind-meld in hopes that it will yield just which repressed memory is causing such a physical reaction in Tuvok - until something goes wrong and without warning, Sulu and the 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.
As the crew fends off mysterious aliens, the Emergency Medical Holographic program overloads and The Doctor may be lost forever.
When 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.
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 Voyager crew finally arrive home - only they're in the right place at the wrong time, Los Angeles, 1996. Using 24th century technology Captain Janeway and Commander Chakotay desperately search for the answers needed to prevent an environmental disaster, all while trying to blend in on the Venice Boardwalk. Meanwhile, The Doctor is held hostage by Henry Starling, CEO of a computer mega-corporation.
While the U.S.S. Voyager orbits above North America with its weapons and long range transporters 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 Voyager's computer system and downloads The Doctor's program, holds him hostage and reconfigures him with 29th century technology.
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. Q pursues the uninterested Janeway just as a jealous female Q appears to bring Q back to the Continuum. While the U.S.S. 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 powers aboard a stranded starship Voyager.
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 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 starship Voyager crew transports to a 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-ridden 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 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.
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.
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.
When the Voyager crew finds a disabled Borg ship adrift in space and discover 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 and learn what killed them.
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.
To improve his performance as the ship's physician, The Doctor undertakes a personality enhancement project on the Holodeck, incorporating several accomplished historical figures' 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.
When a Nezu planet is bombarded by asteroids and its inhabitants face evacuation, the U.S.S. 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.
After Ensign Kim suddenly exhibits abnormal behavior, he instinctively leads the U.S.S. Voyager to a mysterious planet, the Taresian homeworld. There, a shocking story of his birth is told by members of the almost exclusively female population -- Kim is 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, experiences the beginning and final phases of her Ocampan lifespan and gets a glimpse of the 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 bargained for.
The 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 Starship 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 Maquis leading an insurrection aboard Voyager. When crew members surreptitiously play the program, they are each into the role of a Starfleet security officer who is approached by Chakotay to help the Maquis with the mutiny.
As they approach the heart of dangerous Borg territory, the Voyager crew witnesses 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
