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.
Searching to replenish their dilithium supplies, Voyager encounters the Viidans who assault other races for their organs. Neelix is attacked and his lungs taken. Now it's a race against time to retrieve the stolen lungs and save his life.
When the crew finds a mysterious alien burial ground within an asteroid, a unknown phenomenon that teleports the bodies suddenly transports Kim to another planet where an alien race believes he is a being from the afterlife.
Voyager answers a distress call from a Kazon-Nistrim ship, to find all but one of the crew dead in an explosion. Investigation uncovers the Kazon were experimenting with Federation technology acquired from a traitor on Voyager. The Doctor proves Ensign Seska is not really a Bajoran.
After Harry Kim disappears during his 'Beowulf' holonovel program, Chakotay and Tuvok are sent to investigate and they disappear. Not wanting to lose any more crew-members, the Doctor is transfered to the holodek to investigate.
An encounter with a peculiar nebula suddenly leaves Chakotay brain dead and unconscious. The crew is left with a mysterious but powerful force of onboard that can take over the minds of the crew members.
While Voyager's mixed Starfleet/Maquis crew seem to be working out, a few rogue Maquis are fighting the integration. Chakotay selects the most resistant of the group and Tuvok decides to put the rebels through boot-camp, Tuvok style. Meanwhile, Voyager's bio-neural circuitry is afflicted by a viral infection stemming from Neelix's cooking.