A reptilian scientist trying to prove his heretical theories kidnaps Chakotay and draws the entire crew in conflict between his race's doctrine and the startling truth about its origin.
Crew members are replaced one-by-one with aliens from an unknown race.
B'Elanna Torres discovers a holodeck program where Chakotay and the Maquis rebel against Janeway.
Voyager must pass through Borg space, but the arrival of a new species causes problems.
Janeway and Tuvok work with the Borg and meet Seven of Nine as they work on developing a weapon against Species 8472 in exchange for safe passage through Borg space.
Kes' mental abilities develop to a point where they endanger Voyager.
B'Elanna tries to observe the Klingon Day of Honor after the warp core is lost.
Chakotay helps fight in an alien war.
A hologram contacts Voyager and the Doctor is excited to meet another hologram.
Seven of Nine experiences Borg flashbacks as she attempts to become more human.
The crew have unexplained illnesses as they are closely observed by unseen intruders.
Voyager creates a new Astrometrics Lab, which maps a new course that brings them into contact with a Krenim temporal ship that can erase things from history.
A badly damaged Voyager hides in a nebula as a skeleton crew attempts repairs; meanwhile the Krenim commander proposes a compromise to Chakotay and Paris.
Torres is arrested while visiting a world of telepaths where violent thoughts are a crime.
Aliens steal several key components of Voyager, which are retrieved with assistance from a holographic Leonardo Da Vinci.
Neelix dies in an attempt to sample proto-matter from a nebula. Seven of Nine believes she can revive him using Borg nanoprobes, but Neelix finds it hard to adjust, particularly given that he has no memory of an afterlife of any kind.
The crew of Voyager start to have dreams from which they cannot wake, and only Chakotay can save them.
The Doctor's program is sent to an advanced Starfleet vessel via a vast ancient communications network, but he soon discovers that only he and the ship's own EMH remain to fight against Romulans who have taken over the ship and are attempting to return to Romulan space with it.
A transmission from Starfleet Command gets held at a Hirogen relay station and Janeway sets course to retrieve it.
