Stardate: 54014.4 - Partially transformed into Borg drones, Janeway, Tuvok, and Torres run a covert operation on board a Borg ship to infect the collective with a virus that will free subdued individuals from the hive's control.
Stardate: 54129.4 - A key Borg component in Seven's brain begins shutting down, leading to the possibility that she may be facing the equivalent of a terminal illness.
The crew of Voyager enters the Delta Flyer in a sub-warp race, crewed by Tom Paris and B'Elanna Torres, and events conspire to encourage Tom to propose to her.
Stardate: 54090.4 - An investigation of mysterious attacks on members of the crew uncovers a buried plot involving Tuvok and a Maquis fanatic.
The Doctor's program is stolen and he is forced to work in an alien hospital, where he skillfully manipulates the system to provide ethical medical care.
A hologram of Reginald Barclay is sent to Voyager, supposedly to implement a dangerous plan to bring them home; but the hologram has been tampered with by some Ferengi, who are trying to steal valuable Borg nanoprobes from Seven of Nine.
During an emergency on a mission, The Doctor is forced to upload his program into Seven of Nine's Borg implants, allowing him to experience real sensations for the first time.
Stardate: 54274.7 - Ensign Kim finds himself making the hard choices of mission commander when he agrees to help the crew of a ship in need.
Stardate: 54337.5 - Voyager answers a distress call from a Hirogen outpost – only to find carnage caused by holographic technology that Captain Janeway has given them.
Stardate: 54337.5 - Voyager secretly trails two Hirogen ships in pursuit of the renegade hologram ship. Iden, the band's self-appointed leader, begins showing signs of delusional behaviour when he considers himself as the 'saviour of his people', and believes that his people will worship him as a God in their new settlement. With Voyager and the Hirogen ships trailing close behind, the Doctor and Torres must find a way to disable the ships and the holograms before they come under attack from the
Voyager is fractured into several time periods by an accident, and only Chakotay is able to move between them, in the process meeting old friends and old foes from the previous six seasons.
Now married to Tom Paris, B'Elanna Torres discovers she is pregnant. The Doctor tells her to expect a daughter; but B'Elanna's unresolved fear of the childhood traumas, which she suffered as a part-Klingon girl growing up among humans, makes her determined to remove her child's Klingon DNA.
Prisoners are brought onto Voyager from a damaged alien vessel, and the crew must deliver them to their destination – for execution. Seven's nanoprobes are used to help heal a prisoner.
Voyager encounters an ancient Klingon battlecruiser. The Klingons aboard it had set out long ago to find their savior, and they believe it to be Tom and B'Elanna's unborn child.
Voyager is pulled into a void, where the ships that have become trapped attack each other for food and resources.
The Voyager crew is brainwashed into taking new jobs on an industrialized planet that has a severe labor shortage, leaving only Chakotay, Kim and Neelix (who were on an away mission) and the Doctor (who, in the absence of the crew, has become the Emergency Command Hologram) to save them.
Chakotay and Neelix take jobs on the new planet, and try to rescue their amnesiac crewmates – who don't want to leave.
Stardate: Unknown - Seven of Nine runs a series of holodeck simulations to explore her untapped emotions.
Stardate: 54704.5 - Q comes to Voyager and asks Janeway to help him teach lessons of responsibility to his troublesome son.
Stardate: 54732.3 - When the Doctor arranges to have his recently completed holodeck novel published in the Alpha Quadrant, certain aspects of the story hit too close to home among his shipmates.
Stardate: 54775.4 - The Voyager crew, on a mission to track down a historic Earth probe designed to contact intelligent life, finds the probe had indeed crossed paths with another civilization, but with catastrophic results.
While visiting the planet Ledos, Seven and Chakotay crash through an energy barrier. The two are stranded in the jungle with primitive humanoids, who take the pair in and care for Chakotay's injuries. To rejoin Voyager, he and Seven have to disable the energy barrier.
Stardate: 54868.6 - Neelix finds he must make hard choices when he becomes involved in the struggle of Talaxian refugees whose home in an asteroid belt is threatened by alien miners.
Stardate: 54890.7 - The Doctor is forced to carry out a secret mission where he must impersonate members of the Voyager crew.
Stardate: 54973.4 - Twenty-six years in the future, a regretful Admiral Janeway hatches an audacious plan to bring Voyager home sooner, rather than have it spend an additional sixteen years making its journey.