Stardate: 51003.7 As part of the agreement for Voyager to help the Borg fight Species 8472 in exchange for safe passage through Borg space, Janeway agrees to journey onboard the escorting Borg cube.
The Borg want to implant links to the crew, but Janeway balks, insisting that the Borg instead supply a drone to act as their contact. The Borg agree and choose an assimilated human known as Seven of Nine to monitor the crew.
Can Voyager fight off Species 8472 for the Borg? And, can the Borg be trusted not to assimilate the crew if they can?
Kes begins to go through a transformation to a higher plane of existence. However, this transformation puts Voyager in danger. Kes decides she must leave in order to preserve the crew. But, once transformed, Kes imparts a major gift on Voyager and its crew.
Meanwhile, Seven of Nine fights Janeway's attempt to adjust her back into humanity.
Voyager attempts to create a Borg-like transwarp conduit with the help of Seven of Nine. During the first test, things go wrong and Torres must eject Voyager's warp core.
Torres and Paris are sent in a shuttle to retrieve the core, but find ships of the Caatati, a people ravaged by the Borg and with little to live on, about to salvage the core. The Caatati fire on the shuttle severely damaging it, but Paris and Torres are able to beam out into space before the shuttle explodes.
Janeway must negotiate back the core from the Caatati and find the two missing crew before they run out of air.
During her time with Paris floating in space, she realizes she has succeeded in passing through her Klingon Day of Honor, an annual day of self examination, and can now openly express her feelings toward him.
Stardate: 51082.4 Chakotay comes under fire while on away mission and has to emergency beam out to the nearby planet. There he finds the inhabitants are at war, and he is forced to join a side in the conflict. Although Chakotay thinks he has joined the right side, all it not as it appears.
Stardate: 51186.2 When Voyager finds a ship in distress, they are surprised to find the only remaining crew is a hologramatic maintenance man. Upon further investigation, the crew begins to question if what the hologram has told them about the crew's fate is really true or not.
Stardate: Unknown Voyager attempts to negotiate safe passage across another region of space forbidden to outsiders by a race called the B'omar. At the same time, Seven of Nine starts having nightmares of being assimilated and then her Borg implants start to reassert themselves.
When Seven of Nine leaves the ship in a shuttle and heads into the forbidden region of space, Janeway must send a rescue shuttle to find her before the B'omar do.
Stardate 51244.3 An unknown and unseen force is causing medical changes in Voyager's crew. Janeway has terrible headaches, Chakotay, Neelix and others show signs of devastating changes to their DNA.
Even though his program becomes deactivated, the Doctor reaches out to Seven of Nine for her help in finding out what is going on. He modifies her implants to allow her to see those causing the medical changes, but she must remain quiet about what she sees, as know one would likely believe her.
It's now up to Seven of Nine to save Voyager from this unseen attack, before the crew suffers irreparable bodily damage.
Stardate: 51268.4 - Voyager comes under attack from a Krenim Temporal Ship that alters the course of evolution by wiping out entire species from the timeline.
Stardate: 51425.4 With Chakotay and Paris taken by the Krenim temporal ship, Janeway and crew find themselves in a tenuous position. The continuous pummelling that Voyager has received over the last few months have taken its toll on the ship. The Starfleet crew has struggled through the unending attacks in order to survive. Finally, unwilling to give her crew a death sentence, the Captain orders her family to abandon ship. Giving them the directive to set their escape pods' flight path for the Alpha Quadrant, Janeway tells her crew to build new alliances in the hopes that someday they will be reunited again.
Stardate: 51367.2 - The crew takes shore leave on a planet inhabited by a telepathic species that have forbidden all unhappy thoughts and actions. B'Elanna is arrested when she thinks of retaliation to an incident, but a surprising discovery is made when Tuvok starts investigating.
Voyager is set upon by unknown spaceships, which are able to beam off many of Voyager's technological components. The crew must recover these components if they are to continue on their journey home.
They trace their stolen merchandise back to a planet of traders. However, getting it back will not be easy, as the marauders have put the stolen technology to some use on the planet.
Stardate: 51449.2 While on an away mission to collect samples of proto-matter from a nebula, Neelix is killed by a discharge from the nebula. Janeway, believing Neelix' death is final and is preparing for his funeral, is stunned to hear Seven of Nine tell her that Neelix' death can be reversed. She tells Janeway that it is not too late for her Borg implants to resuscitate him. Janeway reluctantly agrees, and Neelix is revived, but the results lead to consequences none of them expected, and which they may not be able to correct.
Stardate: 51471.3 After most of the members of the crew start experiencing similar dreams about an unknown alien, some of the crew cannot be awakened. No one seems to have an answer to this situation. Chakotay then decides to try an ancient Indian technique of directed dreaming to see if he can solve the dilemma. What he finds is a angered race of aliens, who exist in the dream state, and want to extract revenge for their perceived suffering, on the people in the conscious realm. Chakotay must convince the aliens to stop and reverse their actions, at least until Voyager is out of their space.
Stardate: 51462 When Seven of Nine locates a massive communications array, Voyager tries to use it to communicate with the Alpha quadrant. When their attempt fails, they realize they may be able to successfully send a holographic message, using the Doctor's program.
However, the Federation ship in the Alpha quadrant the Doctor is sent to, is under attack by the Romulans and the crew is dead. The Doctor is determined to fight off the attackers, but the ship's holographic Doctor isn't as brave as Voyager's Doctor in this matter.
Stardate: 51501.4 - Voyager starts receiving messages from Starfleet through the communications network, now that they know that the crew is alive in the Delta Quadrant. Some bad news is received by some of the crew, particularly Captain Janeway among others. After a short while, the messages become lodged in one of the modules, and the crew must retrieve them. Shortly, they are crudely introduced to a new enemy, the Hirogen, who seek nothing more than to hug victims for the thrill of the hunt, and Voyager is their next target.
Stardate: 51652.3 When a derelict ship with a lone surviving Hirogen hunter is found, Voyager learns much needed information about their foe. However, what they learn creates more bad news: They find this Hirogen crew was hunting the deadly Species 8472, which the Borg fear above all else. In order to survive this encounter, the Voyager crew must step in and try to stop both species.
Stardate: 51658.2 While Seven begins assisting a trader named Kovin in the instillation of a new weapons system on Voyager, Seven strikes Kovin after he pushes her aside. Seven begins to show signs of anxiety. The crew's investigation into Seven's erratic behavior, leads them to Kovin's lab on the planet, and what happened to Seven there.
But are the facts leading them to the right conclusion, or to a false accusation against Kovin?
Stardate: Unknown The Hirogen take over Voyager, implant neural implant into the crew, and then use them in WWII battle simulations, where the Voyager crew act as the Allied force and the Hirogens act as the German force. The Doctor is forced to treat the wounded crew, in order to keep the Hirogen prey alive. However, when Seven is wounded, the Doctor uses her Borg implants to alert her to the real situation going on.
Seven, now aware of the Hirogen presence, must work to defeat them, while the other Voyager crew are convinced the conflict is real. Seven must do this without making the crew suspicious about her actions, as they may see her as a traitor.
Stardate: 51715.2 The battle continues in Voyager's holosuites, but now both Janeway and Seven are aware that they are part of a simulation. Fortunately for them, it seems that the Alpha-Hunter of the Hirogen has had a change of heart about his quarry. The holosuites have opened his eyes to a new future for the predators known as the Hirogen.
Stardate: 51762.4 Tom Paris, who has been unusually moody, has his spirits lifted after Voyager rescues a pilot and his spacecraft when it gets into trouble. Paris asks to work with Steth, the pilot, to repair the advanced co-axial warp drive on his ship. After the sip is repaired, Steth pulls a fast one by switching bodies with Paris. Paris, now unconscious, is sent away in the ship, and Steth, in Paris' body, is left to live his life out on Voyager.
Stardate: 51781.2 Everything is running normal on Voyager when Janeway suddenly receives a coded message from the ship. It's the highly secretive Omega Directive, which orders all Star Fleet Captains to stop everything, and do everything in order to destroy a detected Omega molecule.
Seven is the only member of the crew Janeway tells about this directive, in the hope that Seven can help her with this task, but Seven decides it might be better to study the highly unstable molecule. This leads to near disastrous results for Voyager.
Voyager comes to rescue of a wounded female in a ship with a cloaking device. The alien, Kellin, immediately asks for asylum from her people. She also tells them that she has been on board Voyager before, but that they can't remember her because her xenophobic race secrete a pheromone the causes a loss of short term memories in others.
Soon, her people come looking for her, firing on Voyager from their cloaked ships. They are determined not to allow any members of their society to ever leave permanently. Can Voyager risk the ship and crew for this one lone asylum seeker?
It is 700 years in the future and Voyager has become museum piece on display by Kyrian race, in the Delta Quadrant. They visitors there are told how Voyager and crew caused the civil war 700 years ago between the Kyrians and the Vaskans, which nearly wiped out the Kyrian race. They are told how Voyager wiped out millions of Kyrian, after taking the Vaskan's side.
However, this view of history becomes challenged when a scientist reactivates the Doctor's program; but can the Doctor prevail against 700 years of strongly held beliefs? The more he tries, the more strife begins to grow between the Kyrians and the Vaskans.
When Voyager finds a planet with much needed deuterium, the bad news is the planet is classified as a "Demon Planet" due to its toxic and deadly atmosphere. After failing in their attempt to beam up the deuterium, Paris and Kim volunteer to go down to the planet and mine the material themselves.
However, both their environmental suits fail, leaving them near death, as Voyager hurries to rescue them. When they locate the two, both are alive and well, existing on the planet without their suits on! When they are brought back onboard, they quickly find the ships atmosphere is killing them. Paris and Kim find they can only survive in the planet's atmosphere, something Voyager can't provide all the way back to Earth. But is there a different reason the two can only survive under the planet's atmosphere? The answer shocks the crew.
When Voyager enters a nebulous area of space with extremely high radiation, the crew finds they have a choice; put the entire crew into protective stasis for a one month journey through the nebula, or take a year and divert around the vast area of space. Only Seven of Nine and the Doctor will be able to remain awake a journey through the nebula. Capt. Janeway decides to trust the ship and crew to Seven and the Doctor, but the trip through the nebula soon shows signs of affecting Seven more than was thought. The question becomes, can she hold on to the control of her faculties long enough to make it through the long journey, with only the Doctor as her companion?
When a visitor with great computer and computational skills asks Voyager for passage onboard, they agree. They ask for his help on the scrambled incomplete Starfleet message they had previously received. The mysterious passenger proves very successful in retrieving the lost portions of the message, including the fact that the Federation has sent an unmanned vessel they need to travel to, that can return them home in no time at all. However, is this miraculous confluence of events too good to be true, and does their visitor have his own secret agenda?