On a mission to the Badlands, the USS Voyager, along with a Maquis ship, is stranded in the Delta Quadrant, more than 70,000 light-years from home by an incredibly powerful being known as "Caretaker."

Tensions rise between the merged starfleet and maquis crews. Investigating an apparent distress call, Voyager becomes trapped inside the event horizon of a quantum singularity.

The Voyager crew discovers a planet which recently suffered a horrific catastrophe. Upon investigation, Janeway and Paris are sent back in time before the disaster and are faced with the decision of whether to try to stop it.

Neelix's lungs are removed by a race that suffers from a deadly phage that is slowly destroying their population prompting them to harvest replacement organs and tissues from other species.

Voyager becomes trapped in a strange nebula when the crew searches for a new power source for the ship.

Voyager makes contact with a Romulan ship through a wormhole that leads back to the Alpha Quadrant.

Tom Paris is convicted of murder. He denies having committed the crime, even though the images extracted from the victim's own memory seem to prove his guilt.

While investigating mineral deposits on an asteroid, the crew finds a mysterious alien burial ground. Harry Kim is transported to an alien world at the same time as a dead woman's body arrives on Voyager.

The crew of Voyager discovers a planet that has the technology to send them more than halfway along their journey home. However, the planet's inhabitants are more than reluctant to share this technology with Voyager's crew, as doing so would violate one of the society's own prime directives.

A fatal disaster aboard a Kazon ship reveals mishandled Federation technology at its heart, which indicates a traitor aboard Voyager.

When several crew members disappear inside Harry Kim's "Beowulf" holodeck program, the holographic Doctor is the only one who can rescue them.

A shuttlecraft with Chakotay and Tuvok aboard is attacked; Chakotay is left brain-dead, while Tuvok begins acting strangely. An unknown force begins controlling crew members.

In an attempt to develop a cure for the Phage, a Vidiian doctor captures Torres and splits her into her 2 halves, one human. the other, Klingon.

Neelix is diagnosed with a fatal illness by a Haakonian named Jetrel. The same man who'd developed a doomsday weapon which destroyed a Talaxian moon and killed Neelix's family.

As Neelix's cooking sickens Voyager itself, Tuvok runs the four most problematic Maquis malcontents through a Starfleet-style boot camp.