The episode commences with the wedding of Torres to Paris. Then a plasma conduit becomes distorted. B'Elanna and Seven discover their enhanced warp drive, which is set to take them back to the Alpha Quadrant in two years, is emitting a subspace field causing molecular decohesion. Shortly thereafter, B'Elanna becomes violently ill. When Paris brings her to sickbay, it is already filling with other sick crewmembers. The Doctor finds that B'Elanna's cellular structure is breaking down, and she is deteriorating. He is powerless to do anything for her except make her comfortable. Paris barely has time to say goodbye to his wife before she dies.
Chakotay and Tuvok look into Voyager's recent history to try and figure out what might have precipitated the crew's illness. About a year earlier, they visited a Class Y "demon planet" which was inhabited by a silver liquid biomemetic compound. When they left the planet they allowed the "silver blood" to sample the crew's DNA and populate the planet with copies of themselves. When the Doctor runs tests on her body, injecting a dichromate catalyst, B'Elanna disintegrates into the metallic compound. The crew realizes that they are the duplicates. The ship itself has been duplicated as well, and the subspace field created by the enhanced warp drive has initiated the slow disintegration of the crew, the ship and its contents.
Captain Janeway finds it unrealistic to try and retrace thousands of light years to return to the demon planet, so she keeps an eye out for another, similar planet of Class Y where they might be able to prevent the degradation of the ship and their own bodies. The planet's atmosphere may be the only thing that will keep them alive. As soon as sensors detect a Class Y planet, they set a course. They cannot get near it, however, as there is a vessel there that warns them off with phaser fire.
Voyager retreats and Janeway orders the crew to look for another class Y planet. Chakotay starts to question her command. The crew is beginning to remember what it was before Voyager came, and their home is the original demon planet. They insist Voyager turn back and try to reach home. Chakotay begins to destabilize and is the next crew member to die. Close to death herself, Janeway decides to bring the enhanced warp drive back online and turn the malfunctioning ship around and set a course for the original demon planet as he wanted.
Still a few weeks out from the planet, Janeway finally dies. Acting captain Harry Kim tries to hold the melting ship together and mobilize the few remaining crew, including Seven of Nine. He understands that Voyager will not make it back to the demon planet, and the only thing left to do is to store all of the ship's computer files in a signal beacon so that perhaps someone might find it someday and the crew's lives will not be forgotten. Unfortunately, the ship is failing to respond, its systems too far disintegrated. Shortly before they die, Kim and Seven detect a vessel nearby, and hope to communicate with it. Voyager will not respond to commands to drop out of warp, so they attempt to eject the warp core to bring the ship to a stop. It is their final action, as the force of the ejection system disintegrates the ship completely.
The approaching vessel is the real Voyager and her crew. They pick up a strange, indecipherable signal on sensors and come across a cloud of mysterious metallic liquid debris. The crew are mildly curious about the odd liquid, but since there is nothing to investigate, they make a quick note in the ship's log and go on their way.