Janeway goes on a hunt for the U.S.S. Equinox who has gone against everything they, and she, was taught by the Federation. Seven and The Doctor are hostages on board the Equinox, and must devise a plan to escape. Janeway goes nearly to the point of insanity, and Chakotay almost instigates a mutiny. Janeway disregards all advice and becomes quite seperated from her friends. The Equinox Doctor, swapped at the end of Part 1, continues in Voyager's sickbay, and the crew are unaware that he his programed to inflict harm on them. Our Doctor, captured on the Equinox, has his ethical subroutines removed, and is ordered to perform surgical procedures on Seven of Nine.
A visit to a Markonian Outpost brings Seven of Nine into contact with her former Borg crewmates, Two, Three and Four of Nine, who wish to access her memories in order to recall their break from the collective. When Seven of Nine is confronted by the three former Borg drones, she also unlocks a dark chapter to her past. After gaining freedom from the collective, Seven was responsible for the re-assimilation of herself and several others, who now seek freedom, even though it may cost their lives -- and Seven's!
Torres confronts a dark side of her Klingon ancestry when she asks a skeptical Janeway to allow doctors to induce a coma-like experience that will allow her to aid her condemned mother who is held aboard a mythic Klingon death barge. Following her bumpy shuttle landing, a groggy Torres discovers an ancient Klingon artifact on board that strangely connects her to her hated warlike heritage. When she is transported to the horrific barge of dishonored souls, Torres learns that her ashamed mother bears the burden of her dishonor, and after returning to the U.S.S. Voyager, she wants to go back for her - even if it means exchanging her own life.
The Doctor files a grievance with Janeway, claiming that the crew is excluding him and treating him rudely. The captain is mystified by the hologram's uncharacteristic behavior, and numerous crew members notice that the Doctor is becoming inattentive, almost as if he is daydreaming. Unknown to his crewmates, the Doctor has altered his program to allow daydreaming, but something destabilizes his program and he begins to daydream at an alarming rate, even in the middle of vital duties. His imagination conjures up numerous unlikely scenarios, from the women of Voyager's command crew battling for his attention, to the destruction of an attacking Borg vessel by the 'Emergency Command Hologram.' Eventually, the Doctor's imagination is in constant overdrive, and Janeway relieves him of duty. But when the Doctor realizes that he is being tampered with by an inquisitive alien, will he be able to convince the crew that this potential threat is no figment of his imagination?
Voyager accidentally drifts into a sub-space corridor and is attacked by the Turei, a territorial race whose armada forces Janeway and her crew to take shelter on a ravaged planet-where they encounter another warlike species whose survivors are encased in bio-pods awaiting 're-animation.' Escaping from the superior force of the Turei, Janeway makes repairs while on a planet whose civilization lies in ruins save for a few hundred stasis chambers holding the slumbering remnants of the Vaadwaur, an ancient culture thought to be extinct. While the captain seeks to form an alliance with the Vaadwaur against the persistant Turei-and promises to find them a new home-she soon senses that her new allies within might pose a greater threat than the enemy she knows is circling above.
Voyager happens upon a scrapyard in space operated by a gangly and gregarious alien called Abbadon. A trade agreement is quickly reached for several small items and technologies, until Tom Paris sets his eyes on a sleek (but very derelict) shuttle-sized vessel. Tom persuades Chakotay to offer Abbadon a few extra items in exchange for the ship - and the alien asks for suspiciously little in trade. Tom begins spending all of his off-duty time - and most of Harry's, too - restoring the mysterious ship to full working order, dubbing it 'Alice' in honor of a cadet he lusted after in Starfleet Academy. Slowly, thanks to the little craft's direct neural interface with its pilot, Tom becomes more and more fixated on 'Alice'...but what he does not realize until it far too late is that the ship is equally fixated on him.
During negotiations with the Kesat government, Tuvok is zapped by a powerful energy force, suffers severe neurological trauma and emerges as a mere shell of his former self while Janeway searches for the mythical species responsible for the attack in hopes of finding a cure. While the optimistic Neelix keeps pushing to restore the mental prowess of the confused Tuvok, Janeway works with Naroq, a Kesat inspector, as they try to solve the enigma of the cloaking device used by the hostile Ba'Neth -- or 'shadow people' --who seek Voyager's technical data. Even as the crew pursues the elusive Ba'Neth for a solution to Tuvok's misfortune, the suddenly vulnerable Vulcan discovers emotions he never could appreciate before.
The Voyager is nearly consumed by a massive rolling ball of energy but curiosity about the rare phenomenon prompts Janeway to launch a probe to investigate and search for a missing 300-year-old U.S. spacecraft trapped inside-a risky maneuver that may cost the lives of the shuttle crew. As Voyager shadows the powerful anomaly known as the Graviton Ellipse, Seven of Nine reluctantly joins a fascinated Paris and Chakotay on the shuttle as they look for the legendary Ares Four, the command module from an early manned mission to Mars. However, once found, the attempt to retrieve the craft and its noble dead pilot proves treacherous, and the small crew must improvise if they are to return at all before the ellipse disappears again into lethal subspace.
When Voyager encounters an alien whose space 'catapult' can speed them back home, a data-overloaded Seven of Nine causes chaos when she incites a civil war then divides the crew with secret allegations of treachery and insurrection. While Janeway debates accepting the use of an alien's technology that can cut their trip back to the Alpha Quadrant by years, an earnest Seven of Nine processes accompanying information and convinces Chakotay that the captain is sabotaging the true mission of Voyager. Likewise, she privately informs Janeway of a budding rebellion, mysteriously fanning flames that threaten to tear the ship apart.
Lt. Barclay is part of something called 'Project Pathfinder', which is charged with bringing home Voyager from the Delta Quadrant. The project idea is to open a small artificial wornhole near Voyager and hold it open long enough for the ship to see it and come through. But the project leaders want to know how the crew will react to the opportunity , and how they might present it to maximize the probability that Voyager will take it. So Barclay (now married) sets up a holodeck simulation of the Voyager crew, running through various permutations to test their viability. As he does, he becomes obsessed with them, regressing back into his holo-addiction. The holo-addiction takes over Barclay's life, threatening his marriage, etc. and Counselor Troi is brought in to snap him out of it for the second time.
Captain Janeway and her crew enjoy some hard-earned leisure time in the holographic setting of a charming Irish village where she can't help falling for a ruggedly handsome townsman-but their holiday is darkened by an approching wave of deadly neutron radiation. Created by Paris as a diversion for himself and his mates, sunny Fair Haven offers Janeway a deceptively realistic fantasy figure named Michael, whose physical and intellectual specifications are made to order for her. Soon, her attention is commanded by the trailing edge of a speedy wavefront that poses more of a threat than anyone knows.
Voyager is trapped above a planet whose energized core permits extremely rapid evolution. Though the planet initially appears to be primitive, the presence of Voyager affects its development, and the world evolves from a 'stone-age' type civilization to a warp-capable society within hours before our very eyes. While Voyager orbits the planet and civilizations rise and fall in a matter of moments, generations of scientists try to figure out what the unusual object in the sky orbiting their world is and try to make contact with it. When Janeway briefly transports The Doctor to the alien world, she learns that the presence of Voyager has inspired invention among the society, which without warning, aims its own weapons at Voyager.
The Doctor's ego soars when Voyager engages an advanced but arrogant race which is entranced by the medical officer's passable singing talent, granting him instant rock-star status. Janeway and the crew are perplexed by the effect that The Doctor's voice and variety of song selections have on such a superior alien culture as the Qomar. Millions of them mob his concerts, countless 'fan mail' messages arrive and groupies abound, but one particular female Qomar catches the good Doctor's eye, and he ponders resigning his commission to stay behind.
When Chakotay, Paris and other crewmen arrive back from a two-week planetary exploration, they each succumb to horrid flashbacks depicting the wartime extermination of Nakan colonists, an occurrence in which they are involved. When Janeway and other crew members begin to fall victim to the same malaise, she retraces the team's shuttle route in search of answers - while hoping that her worst fears of the crew's involvement in war crimes are not proven.
While on shoreleave, Chakotay and Torres attend a Tsunkatse match in a nearby alien world. In the meantime, Captain Janeway is off touring a planet in a neighboring system. Meanwhile, Seven of Nine and Tuvok ask Chakotay if they can study a micro-nebula on an away mission. Chakotay grants them permission. While in the shuttle, Seven of Nine and Tuvok are captured by an alien vessel. An alien named Penk welcomes Seven of Nine to Tsunkatse, telling her that she is going to be a very popular attraction.
Chakotay, Kim, Paris and Neelix are taken hostage when the Delta Flyer is captured by a Borg Cube. The Borg will return the crewmembers in exchange for Voyager's navigational deflector. However, Voyager will be unable to go to warp without it. Seven of Nine tells Captain Janeway that the Borg most likely want Voyager's deflector in order to contact the Collective because their own is damaged. While stalling the Borg, Janeway tells them that she is sending Seven over to make sure that her crewmembers are unharmed. Aboard the Borg Cube, Seven discovers that it is manned by neonatal Drones, or children. The children insist that the Borg will come for them once their link is re-established. Because Voyager cannot give up its deflector, Janeway offers Seven's services in repairing the Cube's technology. One of the Borg children tells Janeway that she has exactly two hours before one of the hostages dies. While speaking with the Borg children, Seven tries to jostle their memories in hopes that they will turn away from the Collective and come aboard Voyager.
Problems begin to arise when Voyager runs a Holodeck program non-stop. Characters within the holographic re-creation of Fair Haven become suspicious of the Voyager crew when they begin to notice strange, otherworldly happenings. The city of Fair Haven is set within 19th century Ireland. After several incidents in which Fair Haven residents observe Voyager crew members use 24th century technology, the townsfolk gather and exchange the similar stories. As the townsfolk begin to recognize that their existance is not what it seems to be, the safety of anyone from Voyager visiting Fair Haven is at risk.
To the shock and disbelief of the crew, their colleague, Ensign Lyndsay Ballard, returns to the Starship after having been killed on a mission long ago. Pursued by her alien Kobali abductors, whose reproductive system is centered on reanimation of the dead, she rekindles her former relationships with Janeway and the crew of the Voyager, hoping to reverse the effects of the alien genes implanted in her system. Her old friendship with Lieutenant Harry Kim ignites and deepens until the moment in his quarters when she realizes the horror and extent of her Kobali genes. Harry's support and affection complicates Ballard's final decision as to whether she will remain human or return to the Kobali homeland with the alien family that loves her.
The oldest of the Borg children, Icheb, is reunited with his parents. He does not want to return at first, and Seven doesn't want him to go as she has become attached to him. He also turns out to be quite smart and could be a major help to the Voyager and her crew. He invents a device to scan for wormholes and the like at a miniature 'science fair' aboard Voyager. He eventually decides to stay with his parents. However, one of the kids clues Seven in that Icheb's parents lied when they relayed the story of his assimilation. Voyager returns to the planet to find that he has been set out alone and unconcious in a shuttle designed to attract the Borg. Further investigation reveals that he was geneticallly engineered to be a 'Borg Killer' and that he was responsible for the virus that killed all the Drones in the Cube back in 'Collective'.
Upon completing a routine shipwide efficiency analysis, Seven of Nine determines that three of Voyager's young crewmembers are unable to perform at acceptable levels. Normally after six months or a year, a crewmember that has been assigned to a Starship will simply be reassigned to a less challenging Federation vessel if their limitations cannot be corrected. However, this is not an option since the three crewmembers are stranded in the Delta Quadrant on Voyager.
A band of Delta Quadrant con-artists have stumbled across the greatest scam of their careers Impersonating Captain Janeway and her senior officers. Using their new identities, they move from system to system engaging in a series of lucrative deceptions. Eventually, the real Captain Janeway and her crew are blamed for these deceptions when the con artists do not deliver the goods as promised. Ultimately, the Voyager crew must either bring the imposters to justice, or pay for their crimes.
B'Elanna Torres takes center stage, literally, when an alien poet finds her alone and unconscious following a crash landing of the Delta Flyer. This writer/director of plays has a life and death need to sway his warlord king through theatre work, wherein Torres' life aboard Voyager becomes an ideal plot line for his pacifist cause.
Seeking revenge against Captain Janeway, an angry crew member, Kes, returns to Voyager in an aged form of herself, with powers to cripple the vessel and everyone in it. Kes travels three years back in time and finds past Kes in the aerponics bay, sedates her, and takes her place amongst the crew.
Voyager's Doctor travels 30 thousand light years to apply an otherwise unknown medical technique to his dying creator, a very reluctant and contentious Dr. Zimmerman. But saving Zimmerman's life almost costs him his own holographic existence. The Doctor transmits his program back to the Alpha Quadrant in order to save the life of his creator, Dr. Lewis Zimmerman, with the help of Reginald Barclay and Deanna Troi.
Neelix, in charge of pacifying the children when lights on the ship flicker and fail, lets his imagination run wild, and turns reality into a fantastical, and utterly believable story which mesmerizes them into believing that a ghost actually dwells on deck twelve As Neelix tells it - an electromagnetic life form takes possession of the ship, shutting down all life support systems, while trying to communicate to Janeway its need to return to the nebula from which it came. Area by area is cordoned off by an invisible force field, and injected with poisonous gas, while the captain sets up an emergency command post in the Engineering Room.
Seven of Nine dreams of a beautiful forest. It turns out that this is a real subconscious realm inhabited by the minds of Borg drones during regeneration periods. Only one in a million drones has the recessive gene required. In Unimatrix Zero the Borg revert to their individual selves. While out of regeneration, they act as normal drones and have no memory of their time in Unimatrix Zero. The Borg Queen knows about Unimatrix Zero and sees it as a disease. She immediately begins to destroy drones that are discovered to visit there.