Janeway strikes a deal with the Borg to exchange the modified nanotechnology for a safe trip through Borg territory, but almost immediately things go wrong. The Borg attempt to force Janeway into a direct neural link to the Collective, but she instead demands that the Borg choose a single drone to facilitate verbal communication, and a female human Borg called Seven of Nine is appointed. An ambush by Species 8472 destroys the Borg cube containing Janeway, but she, Tuvok and a number of Borg safely transport back to Voyager. The Borg quickly assimilate the cargo bay which they have taken over, and Janeway must recover from injuries she sustained in the attack on the Borg ship. When Seven of Nine demands a change in the ship's course taking it into the heart of Borg space, Chakotay decides to abort the newly-forged alliance with the Borg. Now the crew faces the prospect of a Borg invasion from within, or a violent death at the hands of Species 8472, unless Janeway and Chakotay can overcome their differences of opinion regarding cooperation with the Borg.
Seven of Nine, isolated from the Borg Collective and left behind on Voyager, begins a turbulent process of recovery in sick bay. The Doctor believes that she can regain her human biology and identity, but her assimilation during early childhood will make the process difficult. Seven of Nine begins to experience seizures - the Borg's last line of defense is to kill a drone before another species can try to gain an understanding of its Borg technology. Kes miraculously destroys the offending Borg implant through telekinesis, an ability with which she has not experimented for two years. Seven of Nine reviles the crew's attempt to restore her humanity, even making the accusation that Janeway's forced removal of her Borg enhancements are no better than Borg assimilation. Tuvok resumes his meditative exercises with Kes to focus her new abilities, but she begins to exhibit a terrifying command over the structure of matter itself. Between Seven of Nine attempting to regain communications with the Borg, and Kes' increasing lack of control over her enhanced abilities, the crew may lose friends both old and new.
Voyager encounters a handful of ships carrying the only survivors of a Delta Quadrant race which was all but wiped out by the Borg, and Janeway agrees to the refugees' requests for supplies. The reminder of the Borg's destructive power doesn't help the crew's perception of Seven of Nine, who requests an assignment to engineering. B'elanna, who is already suffering her way through the traditional Klingon Day of Honor, doesn't welcome the former Borg, who has proposed using transwarp flight to speed Voyager's journey. The transwarp experiment fails, forcing B'elanna to dump the warp core into open space - and the Ketati refugees take possession of the core before she and Paris can salvage it via shuttle. And the Ketati would also like Janeway to hand Seven of Nine over to them so they can settle old scores.
Chakotay is stranded on a world torn by war, his shuttle shot down by one of the aggressors. After a reluctantly friendly Voray defender is shot down by the Kradin while trying to take Chakotay back to his shuttle, the first officer has to adopt the Voray's indigenous clothing for cover. That night, he is traveling with the Voray soldiers to their base, in the hope that they will be able to contact Voyager, and sees for himself the way the Kradin dispose of the Boray. Still wary of involving himself in their way, Chakotay is forced to defend himself when the nemesis ambushes his party, and escapes wounded while the rest of the Boray fall in the attack. He makes his way to a nearby village and is cared for until the Kradin attack there, too. On Voyager, Janeway has been offered help in locating her first officer. An ambassador from one of the warring races beams up to discuss the situation, an ambassador who is horrified at the way his helpless people are being preyed upon by their merciless nemesis...an ambassador of the Kradin.
Voyager receives a distress call from a hologram aboard an alien ship who claims that his organic crewmates are dead. Naturally, the Doctor takes a particular interest in this away mission and visits the ship along with Torres. The hologram is a nervous wreck with a great deal of hostility toward organic life forms, which manifests itself in a conversation B'elanna. On Voyager, Seven of Nine is assigned to help Harry with a new project, and Harry goes from dreading her company to seeing her as viable female companionship, although the former Borg is only confused by his flirtations (and scares him with her own direct approach to human relationships). If the Doctor can escape his fellow hologram's murderous obsession, Harry may need his help if Seven of Nine gets her hands on him.
Seven of Nine has been experiencing vague visions about the Borg, including the rather incongruous image of a shrieking raven inside a Borg ship. While Seven tries to deal with these disturbing episodes, Janeway opens negotiations with the somewhat paranoid Bomar race, who only offer the Voyager crew a long, convoluted path through their territory. The talks with the Bomar are made even more difficult when Seven of Nine's Borg nature resurfaces and, after threatening to assimilate Neelix and forcing her way into a shuttle, she escapes and flies right into Bomar space. The Bomar consider Seven's unplanned journey - and Janeway's plans for a rescue mission - to be hostile actions, but nothing can stop a Borg drone when it is receiving a homing signal to rejoin the Borg collective.
The crew begins to exhibit strange medical symptoms and the Borg, Seven of Nine, soon discovers the cause. Voyager's crew are unwilling subjects to an alien race's DNA experiments. The aliens are in an "interphase" allowing themselves and their ships to become invisible to Voyager. Janeway winds up with alien implants and Chakotay grows bald and old. Several crewmembers die as a result of the experiments.
Distressed at the loss of his family and an entire colony of his people by a hostile alien enemy, Krenim leader, Annorax, has mastered time manipulation and can obliterate history, making entire lifeforms and civilizations cease to have ever existed. In this way, he hopes to restore his loved ones by erasing the enemy that caused their deaths. His well-calculated plans are thwarted by the incursion of the U.S.S. Voyager. Captain Janeway and her crew come between Annorax and his plans, for which it seems he will make good on his promise to destroy the starship.
A crippled U.S.S. Voyager, structurally weakened and shattered beyond operation, hides from the pursuing Krenim weapon-ship, in the conclusion of a two part story. Most of the crew has abandoned the U.S.S. Voyager, leaving only a skeletal staff and the determined Captain Janeway on-board. With whole segments of the proud starship missing, and life-support systems failing, Captain Janeway is adamant about defeating the Krenim or going down with her ship.
A visit to the homeworld of the Mari, a race of telepathic beings, gives the U.S.S. Voyager crew a chance for some much-deserved "shore-leave." However, these beings, who have forbidden violent thoughts as well as actions have B'Elanna Torres arrested for involuntarily thinking of an angry retaliation to an incident. Tuvok becomes involved in her case and makes a startling discovery about the Mari.
A small and nimble alien spacecraft attacks the U.S.S. Voyager, using high energy transports to break through the ship's shields, scan its contents and pluck off valuable equipment. Janeway and Tuvok beam down to the pirates' homeworld in search of the ship's main computer. To their surprise, they find Janeway's holographic Leonardo da Vinci, who becomes an essential part of their plans to retrieve the goods and leads them to the pirate king, Tau.
Neelix is preparing a shipboard feast on the eve of Prixin, the Talaxian celebration of family, when he is asked by Chakotay to join him and Paris on a shuttle mission. Neelix is all too glad to help, but the assignment proves to be fatal for him. Upon the shuttle's return to the U.S.S. Voyager, Seven of Nine, citing Neelix's diverse functions within the crew, applies Borg technology to reactivate him. Alive and shaken by his death, Neelix questions his assumptions about life -- and the promised afterlife -- as the Prixin festivities commence.
Many members of the crew report the sudden incongruous appearance of a previously unknown alien being in their dreams. Discussion of the alien's appearance reveals that everyone has seen the same creature, even though no one has ever met this species before. The Doctor fights to keep the crew from falling into comas, but before long he is fighting a losing battle. Chakotay, whose Indian meditation practices include a thorough knowledge of directed dreaming, believes he may be able to lead the rest of the crew out of the alien's trap...but even his abilities may not match up the power of the crew's uninvited guests.
Seven of Nine uses an alien communications relay to locate a Federation starship in the Alpha Quadrant. Janeway decides to send the Doctor through the relay as a data stream with orders to tell Starfleet of Voyager's misadventures. When the Doctor arrives aboard the U.S.S. Prometheus, however, he discovers that the experimental warship has been hijacked by Romulans, and the Starfleet crew are all dead. He can't return to Voyager without drawing attention to himself, so he passes himself off as the ship's holographic doctor when he is discovered. But he discovers that the Prometheus has its own EMH program who is hiding from the Romulans. The Doctor must put his years of unprecedented experience to work to thwart the Romulans single-handedly, while trying to prove to the next generation of the holographic doctor that there's more to life than waiting to be activated in sick bay.
Miraculously, the ship begins receiving messages, transmitted across the vast distances over the same relay system, from relieved family and friends back home. Voyager's crew is elated to finally hear from loved ones after so many years. However, for Captain Janeway and others, their joy is tempered by bittersweet news. Many messages are still being held at the module. Voyager proceeds to the alien craft to attempt retrieval of the remaining transmissions. Tuvok and Seven of Nine are ordered to board a shuttle and inspect the craft. Before they can, however, they are captured, beamed aboard an alien vessel and trussed-up like animals as a rude introduction to the Hirogen, a hostile, alien race of hunters. Living for the thrill of the hunt, the Hirogens have targeted Voyager's crew as prey in their latest game.
Voyager encounters a Hirogen ship, adrift, with a critically wounded Hirogen hunter on board. Janeway orders that the alien be beamed into Voyager's sickbay, despite Seven of Nine's warnings that the formidable Hirogen would regard the crew as no more than prey to be hunted and killed. Janeway disavows her concern and brings the Hirogen onboard. His presence brings even greater danger when the creature that he has been hunting across space -- species 8247, lethal even to the Borg -- boards Voyager.
Kovin, an alien arms merchant, is on board the U.S.S. Voyager to barter his impressive array of weapons with Captain Janeway. As installation of the weapons will require a reconfiguration of the U.S.S. Voyager's schematics, Janeway orders Seven of Nine to assist Kovin. Seven complies, if only to get back into Janeway's good graces after their recent disagreements. However, an altercation between Seven and Kovin brings the Captain to believe Seven is once again non-cooperative - until The Doctor makes a discovery about Kovin and Seven.
Having invaded Voyager and discovered the many uses of the Holodeck, Hirogen hunters have been playing a deadly game with Voyager crew members, putting them through various scenarios in which they are being hunted down as prey. One of the scenarios takes place in occupied France, with the Hirogen as Nazi SS Officers chasing down Captain Janeway, Seven of Nine, Tuvok and Torres as members of the French Resistance.
Implanted with subdermal transmitters, the crewmembers have no knowledge that they have identities beyond the characters they are playing. Only the Doctor, forced to mend the steady stream of wounded crewmembers to sick bay, is conscious of the invaders. He soon figures out a way to disengage Janeway and Seven of Nine, who then must begin to figure out how to defeat the Hirogen at their own game.
U.S.S. Voyager comes to the aid of an alien, Steth, who claims to be the test pilot of a new spacecraft that has run into trouble. Paris, who has become weary of being on the U.S.S. Voyager, volunteers to help him repair his ship. However, Steth is able to copy Paris's DNA and swaps physical appearances with him. Paris is then left behind in Steth's ship while the imposter takes over his duties at the helm and leaves the real Paris behind. It isn't long before "Steth" is confronted by Daelen, another alien who is seeking her original form. Back on the U.S.S. Voyager, Janeway suspects something is wrong, but Steth assumes her appearance and takes command.
The crew is mystified when Captain Janeway begins an important, though highly secretive, operation in response to a strange subspace disturbance. Chakotay finally compels her to tell the crew so that they may help. Janeway explains that Voyager has detected a dangerous, unstable substance called the Omega. The molecule has the power to destroy space and Starfleet's highly classified operating order is to destroy the Omega whenever it is encountered. Seven of Nine speaks out to say that the Borg believe the Omega can be captured and neutralized for study, which puts her in conflict with Janeway's Starfleet mission.
Voyager encounters an alien vessel fleeing attack whose sole inhabitant is a female alien asking for Chakotay to help rescue her. The startled Chakotay leads an Away mission to the damaged ship to help the alien, Kellin, who claims that she and Chakotay met before. Back on board Voyager, Kellin claims to have been on the ship not very long ago and she fell in love with Chakotay. Now fleeing her home planet's repressive government, she seeks asylum aboard the starship. Chakotay, though drawn to her, doesn't know whether to believe her or not.
A curious holographic tableau is on display in a Kyrian Museum and the curator, Quarren, explains to visitors how the intervention of the Voyager spacecraft started an apocalyptic war on a planet inhabited by two species: the Kyrians and the Vaskans. Ethnic rivalries between the two races are still uneasy, seven hundred years after Voyager has come and gone, and some Vaskan visitors are appalled by the Kyrians reconstruction of history based on a few recovered artifacts. But more damaging information is on the way, when Quarren activates a newly discovered device containing active data. This turns out to be the holograph program for The Doctor, who soon finds himself on trial for war crimes attributed to Voyager and its crew over seven centuries ago.
Depleted of resources, Voyager limps into the vicinity of a class Y planet, known informally as a "demon" class planet. Though standard Starfleet procedure calls for total avoidance of the hostile environment of these planets, Janeway and the crew are left with no choice but to try to improvise a way to adapt the planet's natural resources to power Voyager. Tom and Harry are the first away team to visit the planet, and they fail to report back. But the rescue team commanded by Chakotay finds both of them in perfect health - and capable of breathing freely in the deadly atmosphere of the planet. However, transporting the two back to Voyager almost proves fatal, leading the Doctor to believe that anyone who has visited this class Y planet can never leave it again.
Voyager arrives at a vast nebula, and trying to go around the gaseous structure would add months to the ship's journey. But Janeway's command to proceed into the nebula nearly meets with disaster as the crew begins suffering radiation poisoning. Janeway is forced to consider putting the entire crew in stasis and leaving Voyager in the hands of the Doctor and Seven of Nine, whose Borg shielding renders her immune to the radiation poisoning. Though Seven is undaunted by the exhaustive schedule of duties she must perform as the ship's sole pilot and engineer for an entire month, she may be unprepared for the sense of isolation that she must endure - but is she really alone, or has someone else boarded Voyager?
On a routine supply stop, Paris and Neelix meet Arturis, an alien with a gift for translation. As Arturis hitches a brief ride aboard Voyager, Janeway decides to let Arturis try to decipher the encrypted message Starfleet sent through the Hirogen communications array several months earlier. Arturis makes quick work of the message, revealing a set of coordinates and a slightly garbled message from Admiral Hayes of Starfleet, detailing a new hope for Voyager's crew to return home. But it is only when a wary Janeway tries deciphering the message on her own, while trying to convince Seven of Nine to return to the Alpha Quadrant with the crew, that the origins of the mysterious Starfleet experimental ship Dauntless are uncovered. This new ship, left unmanned for Voyager's crew to use, is not on a mission of mercy, but a mission of vengeance.