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In order to bring some rebellious former Maquis crew members into line, Tuvok gives them a crash course in Starfleet discipline and protocol.
The man who designed the weapon that destroyed all life on the moon of Neelix's homeworld, including that of his family, diagnoses Neelix with a fatal illness.
The Vidiians capture Paris, Torres and Durst while on an away mission. Torres is taken to a lab and "split" into two people: one human and one Klingon.
After Chakotay and Tuvok are injured in a shuttle accident, a non-corporeal life form begins to wreak havoc on Voyager by infiltrating the minds of the crew and altering the ship's systems one by one.
Harry Kim disappears from the holodeck during his holo-novel, Beowulf. According to the characters, he died at the hands of a mystical beast known as Grendel. When Chakotay and Tuvok also disappear, the Doctor is transferred to the holodeck to investigate.
When stolen Federation technology is found on a severely damaged Kazon-Nistrim ship, Seska becomes the prime suspect. The evidence is further reinforced when questions arise over her true heritage.
When Voyager is offered shore leave by the Sikarans, Harry Kim discovers advanced technology that would send Voyager 40,000 light years closer to home. However, the Sikaran's "Canon of Laws" forbids them from sharing their technology with anyone.
While investigating an asteroid belt containing a new element, Harry Kim is pulled into a "subspace vacuole" and switched with a dead body. Soon after the body is revived the crew learns that the asteroid belt is the graveyard of an alien culture that transports its dead in the belief that they evolve into a higher state of consciousness. Harry's appearance on the home world begins to raise questions about the existence of their afterlife.
Tom Paris is accused of a murder he claims he did not commit. His sentence is to re-live the last few moments of his victim's life every 14 hours through a memory transplant.
The discovery of a micro-wormhole leading to the Alpha Quadrant allows the crew to communicate with a skeptical and paranoid Romulan. The crew is elated when they believe they might be able to transport to the Romulan ship. However, all is not as it seems.
In the search for omicron particles to boost the ship's energy supplies, Voyager inadvertently injures a space-faring life form.
During an away mission in search of dilithium crystals, Neelix's lungs are removed by a disease-ridden race of aliens known as the Vidiians. As The Doctor attempts to treat him, the crew of Voyager must find a way to track down these Vidiians.
After being hit by the shockwave of a devastating planet-wide explosion, Voyager investigates. While on the surface, Janeway and Paris are accidentally "shifted" one day into the past.
As the Maquis crewmembers begin to integrate themselves into the Starfleet crew, Voyager becomes trapped in a quantum singularity.
While in pursuit of a Maquis ship in a region of space known as the Badlands, the starship Voyager, under the command of Captain Kathryn Janeway, is transported 70,000 light years from home into the uncharted region of the galaxy known as the Delta Quadrant.