Just after B'Elanna and Tom Paris say their wedding vows and prepare for a holodeck honeymoon, Torres discovers a problem in engineering. After further investigation, she finds one of the Jefferies tubes is losing molecular cohesion due to subspace radiation from the warp drive. Suddenly, Torres becomes violently ill. When Paris brings her to sickbay, they find several more crewmembers in the same condition.
The Doctor diagnoses Torres with acute cellular degradation and explains that her chromosomes are breaking down at the molecular level. Meanwhile, Chakotay and Tuvok pinpoint an event that could have caused their problems. They encountered a bio-memetic compound — the "silver blood" — on the Class-Y "demon planet" they visited about a year earlier. When they left that planet, the crew's DNA was copied, and duplicates of themselves stayed on the planet to begin a new population. However, after the Doctor injects a dichromate catalyst into her deceased body, Torres disintegrates into the metallic compound. Chakotay and Tuvok realize they are all the duplicates, and not the "real" Voyager crew.
Unwilling to travel thousands of light-years back to the demon planet, Janeway plans to forge ahead toward the Alpha Quadrant and hopes to find a solution to the rapid degradation. When sensors detect a Class-Y planet, the crew readies the ship to land, knowing that the planet's atmosphere is the only thing that may keep them alive. However, a vessel suddenly appears that warns them to leave and begins firing.
Voyager is unable to sustain the hits from the firing ship and must retreat. When Janeway orders the crew to search for another demon planet, Chakotay tells her they are questioning her command. The crew is beginning to remember their existence before Voyager, and to them, Earth isn't home. After Chakotay's neural pathways start to destabilize, he dies in sickbay. Close to death herself, Janeway decides to turn the ship around and set a course for the demon planet.
A few weeks away from the planet, Janeway dies. As acting captain, Kim tries his best to hold the ship together with the help of Seven of Nine — one of the only other remaining crewmembers — and to fulfill Janeway's request to store the ship's database in a signal beacon so at least the crew's accomplishments won't be forgotten. Failing to accomplish that, Kim and Seven detect an approaching vessel. Kim orders Seven to eject the core so they can drop out of warp and hail it. But the force of doing so causes the ship to disintegrate, and the approaching vessel — the real U.S.S. Voyager — comes across the mysterious debris. Curious about the distress signal they were receiving, the real crew can only make a note of the event in their log.