Voyager finds a solution to combat the invader of Borg space. Janeway asks for free passage through their territory and in return she'll share a biological weapon. Seven of Nine is assigned to work with Janeway and the Voyager crew, but can the Borg be trusted to uphold their end of the bargain.
Kes's telepathic powers increase and she has to make a life changing decision. The Doctor starts to remove Seven of Nines Borg implants, even though she does not want him to, because of her body is starting to reject them.
Torres has a stressful & emotional day with Paris. A race decimated by the Borg, called the Caatati request major assistance from Voyager.
After Chakotay is marooned on a planet where two alien life forms are attempting genocide against each other, he starts to feel sympathy for the aliens who are helping him since he is not of their enemy race. Janeway and the command crew attempt to discover where Chakotay's shuttle crashed.
The Doctor and Torres go on a away mission to a space station after receiving a distress call from a holographic crewman. Ensign Kim and Seven of Nine work with each other again and start to get to know each other.
Seven of Nine's Borg implants begin regenerating after she experiences hallucinations and flashbacks from her life before assimilation. She flees Voyager in a shuttle to attempt rejoining the Borg. After escaping into a region of space governed by the B'omar, she discovers a wrecked Federation spaceship on an uninhabited moon. This ship is the Raven where the Borg assimilated her and her parents 20 years ago.
The Doctor and Seven of Nine discover that a mysterious illness striking down the crew is the work of aliens conducting genetic experiments on crew members.
A renegade Krenim warship with the ability to alter the time stream threatens the crew of Voyager as they pass through what has now become the Krenim empire.
Captain Janeway desperately tries to keep Voyager from being completely destroyed, Paris and Chakotay try to plot how to save Voyager while on the Krenim time ship.
While Voyager's crew is on shore leave on a planet of peaceful telepaths with no crime, one of the world's citizens performs a savage beating. This sparks an investigation and jailing of Lt. Torres due to her voilent thoughts. Tuvok makes friends with the world's police officer, and Neelix becomes interested in a female shopkeeper.
While on their journey home, Voyager is plundered by space pirates, who use a special transporter to steal machinery from passing ships. Captain Janeway and Tuvok pursue them to their homeworld, where the holodeck program of Leonardo Da Vinci helps Captain Janeway get Voyager's items back.
Neelix is accidently killed by a protomatter discharge on an away mission and then "reactivated" by Seven's Borg nanoprobes. He finds himself in a deep existential and spiritual crisis, questioning his faith and the meaning of his existence,
The crew experiences vivid nightmares, all containing the same mysterious alien. Chakotay must stay awake to lead an attack against a species that lives in the dreams of Voyager's crew.
Seven of Nine discovers an ancient subspace relay network that extends to the Alpha Quadrant. They can send the Doctor through to a Federation ship at the other end, the experimental U.S.S. Prometheus, only to discover that Romulans have taken it over.
After contacting Starfleet Command using the alien relay modules to communicate with Earth, Starfleet replies with letters from the crew's friends and family. Using of the alien array attracts the attention of the Hirogen, an alien species that live to hunt other humanoids.
Stardate: 51652.3 - When Voyager encounters a disabled Hirogen ship with a wounded Hirogen aboard, Captain Janeway beams him aboard for treatment. Soon, the prey being hunted by this particular Hirogen, a member of Species 8472, boards Voyager, damaging it. The only immediate solution is to let the Hirogen assist the crew in tracking its prey. Finding the creature severely wounded, Captain Janeway puts it under her protection, much to the chagrin of Hirogen. Seven of Nine disobeys Janeway's order and transports the Hirogen hunter and the creature to another Hirogen ship.
After working with an arms dealer, Seven of Nine starts having mental images of the arms dealer holding her captive and stealing Borg Nanobots from her. Captain Janeway starts an investigation into the matter with the help of the Doctor.
When the Hirogen capture and board Voyager, they discover that they can use the holodeck to improve the hunt by putting the prey through different situations and locations. In one simulation, Captain Janeway, Torres, Tuvok, and Seven of Nine are members of the French resistance in occupied France during World War II, with the Hirogen in roles as Nazi SS Officers. Since the Hirogen implanted the crew with subdermal transmitters, they have no idea this is on the holodeck with the safety protocols removed, and they think it's real. The Doctor in sickbay is forced to heal the injured, and it is up to him to disable the transmitters and help the crew escape.
Captain Janeway, Seven of Nine, and Harry Kim work to shut down the Holodeck simulation set in occupied France during World War II that the Hirogens started and expanded while also trying to restore the rest of the crew's identities.
An identity-stealing alien (or genome thief) switches physical forms with Tom Paris and then takes command of Voyager after assuming Janeway's identity.
Stardate: 51781.2 - Voyager is forced out of warp when it detects the most powerful substance known to exist called "Omega," which only Janeway and Seven of Nine know about onboard the ship. The Borg experimented with "Omega" in the past. Due to the nature of the particle, a top-secret Starfleet directive gives knowledge of it only to Starfleet Captains and orders its destruction at all costs because the unstable molecule has the power to destroy subspace. Janeway must enlist the help of the senior crew on a need-to-know basis to destroy it safely.
A beautiful alien fleeing danger asks for Chakotay's help, claiming they knew each other in the past. She requests asylum aboard Voyager, saying she was on the ship a month ago and fell in love with Chakotay. But neither he nor any of the crew remembers her anymore.
Seven hundred years into the future, a backup version of the Doctor is reactivated and faces trial for war crimes. He must uncover the truth to defend Voyager's crew and set history straight when an alien race claims that the Warship Voyager was responsible for war crimes committed against their race when the ship passed their planet centuries ago.
Stardate: Unknown - In search of the vital chemical deuterium essential to Voyager's energy supplies, they discover a hostile "Demon class" planet with reserves large enough to replenish the ship. Ensign Kim and Tom Paris take a shuttlecraft to the planet's surface in environmental suits. Soon they are found on the planet without suits, and the ship's atmosphere becomes poisonous to them.
Stardate: 51929.3 - When Voyager encounters a deadly radioactive nebula, Captain Janeway decides to save time by going through it and placing the crew in protective stasis chambers to survive, with only Seven of Nine and the Doctor left to protect the ship. Seven soon starts experiencing hallucinations when an alien wants to trade vital supplies.
Stardate: 51978.2 - An alien translator named Arturis can finally decode the Starfleet message received by Voyager five months ago. It directs them to a nearby sector where an unmanned Federation starship waits for them. It's equipped with a propulsion system faster than warp drive, which can bring them home within three months. While the crew members are elated, Seven requests permission to remain in the Delta quadrant. However, everything is not what it seems when alien technology is found aboard the new ship.
