After a decades-long journey to reach the Alpha Quadrant, Admiral Kathryn Janeway makes a bold decision to change the past in an attempt to undo the toll taken on the crew during their arduous journey home.
The Doctor must impersonate various crew members when Captain Janeway is abducted and held hostage for Voyager's warp core.
When Voyager discovers a settlement of oppressed Talaxians living on an asteroid, Neelix feels compelled to help them. As he spends time with his people and starts to forge relationships with them, he faces a very difficult decision.
A strange energy barrier causes Chakotay and Seven's shuttle to crash on a planet inhabited by extremely primitive aliens.
With regular communications to the Alpha Quadrant established, Starfleet sends a mission to Voyager: retrieve a 21st Century probe sent from Earth called Friendship One.
Once the probe is located on a nearby planet the away team is shocked to learn of the impact it has made.
A means of direct communication is established with Voyager allowing each crew member to speak with family and friends. The Doctor sends a holo-novel for publication based on a lost starship with a doctor who is treated like a slave, which causes controversy among the members of the ship.
When Q's son becomes reckless and uncontrollable, Q places him in Captain Janeway's care for a week.
When Seven tries to perfect her social skills on the holodeck, her hobby quickly becomes an obsession, leading her to neglect her duties.
Chakotay must convince Janeway and the other crew members of their past lives on Voyager. Matters are complicated when Chakotay is exposed and taken for interrogation.
When Chakotay, Kim and Neelix return from an away mission, they find Voyager abandoned, with only the Doctor on board. Meanwhile, the crew have unwittingly become part of an alien workforce, while their memories of Voyager have been erased.
Voyager is pulled into an empty layer of subspace where ships are forced to attack each other and steal supplies for survival. Voyager's only hope for survival lies in forming alliances with other ships who wish to escape "the Void".
Voyager encounters a group of nomadic Klingons aboard a generational ship. These Klingons left the Alpha Quadrant over 80 years earlier, in search of a savior who would one day lead them to a new homeworld, and their leader believes that Tom and B'Elanna's unborn child is this savior.
Voyager is forced to evaluate their ethical beliefs, as well as those of an alien criminal justice system, when they rescue a Nygean prison warden, and his prisoners scheduled to be executed.
Tom and B'Elanna are overjoyed to learn that they are going to have a baby. However, after learning that the child will have dominant Klingon features, B'Elanna begins to experience upsetting flashbacks of her own difficult childhood.
After Voyager passes near a spatial rift, Chakotay is injured in Engineering, leaving his body in a state of temporal flux. After receiving treatment in sickbay, he inadvertently gains the ability to pass through rifts in time that are scattered throughout the ship, enabling him to walk into different stages of Voyager's history over the past seven years.
The renegade holograms abduct B'Elanna in hopes that she will be able to make their field generators fully functional. Meanwhile, Voyager secretly trails two Hirogen ships as they attempt to track and hunt down the holograms, in order to rescue B'Elanna.
Voyager receives a distress call from a Hirogen training facility, where their holographic prey have become too cunning and dangerous for the hunters. Voyager establishes a tentative alliance with the Hirogen in order to disable the holograms, while the Doctor finds himself becoming sympathetic to their cause.
While searching for dilithium, the Delta Flyer, under Harry's command, comes to the aid of a ship under attack. Believing them to be on a humanitarian mission, Harry convinces Janeway to allow him to captain the medical transport to its homeworld.
Seven is forced to hide The Doctor's program by downloading him into her implants, when the Delta Flyer comes under attack from the Lokirrim. Meanwhile, on Voyager, Tuvok enters Pon Farr.
A hologram of Reginald Barclay arrives in a data stream with plans to get Voyager home within three days, by traveling through a "geodesic fold". However, the Doctor soon becomes suspicious of the holographic Barclay's behavior.
The Doctor is abducted from Voyager and forced to work in a hospital where patients are treated based on their social status.
Former members of the Maquis fall victim to a spate of mysterious attacks on board Voyager. Tuvok is placed in charge of the investigations, and soon makes some remarkable discoveries.
Paris and Kim enter a race that symbolises a peace treaty between four warring races. Meanwhile, B'Elanna fears that she and Tom aren't meant to be together.
Seven's life is at risk when her cortical implant - essential for regulating her implants and balancing them with her human physiology - starts to degrade. As Captain Janeway and the Doctor try to come up with a way to help her, Icheb realises he may have to take matters into his own hands.
The away team must infiltrate the Borg Collective and execute their plan to undermine them, even though it may destroy Unimatirix Zero forever.
Seven of Nine is led to a place known as Unimatrix Zero; a place where Borg drones are individuals for a short period of time during their regeneration. However, once their regeneration is complete, all recollection of the event is erased. Captain Janeway uses this to form a plan of attack that would create a mutiny from within the Collective.
When Voyager shuts down main power and interrupts the regeneration cycle of the Borg children, Neelix keeps them entertained by telling the story of why a certain section of Deck 12 is off-limits, and how the space-dwelling creature that lives there came aboard and "haunted" the ship.
News reaches Voyager through the up-and-running Pathfinder project that the Doctor's creator, Lewis Zimmerman, is critically ill. In an attempt to save his life, the Doctor's program is transmitted to the Alpha Quadrant, but once there, he finds Zimmerman does not want to be examined by an "obsolete" EMH program.
An older Kes returns to Voyager to take revenge on Janeway for taking her away from her homeworld too young. Using her telekinetic powers to travel through time, Kes intends to deliver Voyager to the Vidiians and "rescue" her younger self.
A poet discovers an unconscious B'Elanna Torres in the damaged Delta Flyer, after it crash landed on his planet. In need of inspiration, this poet intends on using B'Elanna and the stories of Voyager in his plays, to win favour with his warlord patron.