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Voyager comes to the aid of the Equinox - another Federation starship also abducted by the Caretaker - now under attack by mysterious aliens from another dimension. As the two crews begin to work together to protect both ships, a dark secret lies hidden aboard the Equinox.
An alien missile with artificial intelligence takes over The Doctor's systems, and insists that it be allowed to complete its mission of mass destruction.
Seven is recruited by Captain Braxton of the 29th century timeship Relativity to go back in time and stop an unknown culprit from destroying Voyager.
Captain Janeway relates the story of her distant ancestor, Shannon O'Donnell (Kate Mulgrew in a dual role), and her involvement in the construction of Earth's "Millennium Gate". She meets and falls in love with Henry Janeway - the one man standing in the way of the Gate's construction.
The Doctor tries to introduce Seven of Nine to the concept of dating.
After encountering a damaged Malon freighter, a repair crew from Voyager tries to contain a toxic chemical leak that threatens a nearby inhabited planet.
Voyager is ambushed by a race known as the Hazari with no way of escape. Soon, an alien "Think Tank" arrives with an answer to the ship's problem and all they ask in return is Seven of Nine.
Voyager becomes trapped in an area of "chaotic space", where the laws of physics are in constant flux. Meanwhile, Chakotay suffers from hallucinations related to his holodeck boxing program. Although he is afraid he is losing his mind, Chakotay's hallucinations may be Voyager's only hope of learning how to escape from chaotic space.
After Paris and Torres tie the knot, the ship and its crew start to disintegrate on the molecular level.
Without medical clearance, Kim becomes involved in a love affair with a member of the Varo species. Problems arise when they become biochemically interdependent after the incident.
While the Borg Queen tries to convince Seven to willingly rejoin the collective, Janeway mounts a desperate rescue plan to save her captured crewman.
After defeating a Borg ship, Captain Janeway decides to launch an attack on another damaged Sphere to steal a trans-warp coil. However, as the crew prepare for their heist, the Borg Queen is secretly aware of the entire plan.
The crew is elated to discover a wormhole that appears to lead directly to Earth. As they begin to act impulsively, Seven works with Naomi Wildman to save everyone from what she fears is a trap.
When an intense gravity well causes Tuvok, Paris and The Doctor's shuttle crash on a barren planet, they befriend a female alien who had also crashed there years earlier. As the months pass, they give up hope of being rescued. However, aboard Voyager, only a few hours have elapsed.
Photonic life forms mistake the characters in Tom's holonovel for real people, which leads to a war with the holodeck characters.
When The Doctor discovers that his short-term memory has been tampered with, he launches an investigation. However, when the culprit is caught, he is shocked to learn who is responsible, and why.
Janeway must find a way to hide her telepathic officers, as well as twelve telepathic refugees, while traveling through space controlled by the Devore - a species who has outlawed telepathy.
Paris defies a direct order when he insists on helping a people whose maritime planet is in danger of becoming uninhabitable.
When an alien attaches itself to B'Elanna's nervous system, the Doctor enlists the help of a holographic recreation of an expert. However, when B'Elanna learns that the expert is a Cardassian that performed immoral medical experiments during the occupation, she refuses treatment.
After encountering a piece of Borg technology known as a Vinculum which connects drone's minds together, Seven of Nine begins exhibiting the personalities of people that she assimilated as a member of the collective. Soon, they become so strong that they may overwhelm Seven's own personality.
When Voyager uses new quantum slipstream technology in an attempt to get home, a miscalculation causes the ship to crash into an ice planet. Fifteen years later, the sole survivors, Chakotay and Kim, steal the Delta Flyer in an attempt to send a message back in time and avert the disaster.
Neelix is caring for Naomi Wildman while her mother is on an away mission. When the Delta Flyer is forced to make an emergency landing, and it isn't known whether Tuvok, Paris, or Ensign Wildman survived, Neelix struggles with how to shelter Naomi from the bad news.
The crew of Voyager discover a simulation of Starfleet Headquarters being run by Species 8472, being used as a training ground in preparation for an assault on the Alpha Quadrant.
In order to retrieve a probe stuck in a hazardous atmosphere, Tom Paris designs a new type of shuttlecraft. Meanwhile, Torres begins to exhibit reckless behavior, engaging in dangerous holodeck programs without safety protocols.
A transporter accident merges Seven's Borg nanoprobes with The Doctor's mobile emitter and an ensign's DNA to create a 29th Century Borg drone.
Crew morale hits an all-time low when Voyager must spend two years crossing an expanse devoid of any stars or signs of life. As Captain Janeway is forced to reflect on the choice she made stranding her crew in the Delta Quadrant, little does she know, she will face a similar decision when Voyager ends up in the middle of a serious conflict.