The Voyager crew celebrates the wedding of Torres to Lt. Paris, as well as the successful use of their enhanced warp drive that will cut the remaining time to the Alpha Quadrant down to two years. Their celebration is short-lived, as systems across the ship start to fail, and Torres comes down with a crippling disease that is breaking down her cellular structure, eventually succumbing to death. Between The Doctor's findings and readings taken from the various system, the crew quickly discovers that they and the ship are duplicates of the real Voyager crew, created when the ship landed on a Class Y "demon planet" within the last year ("Demon"). The biomimetic compound that makes up the crew and the ship has become unstable within the warp field.
As more crewmembers and ship systems fail, Captain Kathryn Janeway orders the crew to look for another Class Y planet, hoping that exposure to its atmosphere will stabilize the biomimetic compound. They come across one after some searching, but it is protected by a mining ship; though Voyager could destroy the mining ship, Janeway orders Voyager to retreat, putting Starfleet values above their own preservation. With no other choice, Janeway orders the ship to turn around, and engage the enhanced warp drives, hoping to reach the previous Class Y planet before their ship collapses. En route, Janeway suggests the construction of a time capsule of materials not made of the biomimetic material, storing their personal and mission logs in case they do not make it.
Some time later, with only a skeleton crew remaining and much of the ship uninhabitable, the remaining crew realize they will no longer be able to make it to the planet. Attempts to launch the time capsule fail. The failing sensors detect a ship just in communications range, but their communication array is all but non-functional. Harry Kim, now acting as Captain, orders the warp core ejected to bring the ship out of warp and allowing them time to contact the ship for help, knowing this may tear the ship apart.
The real Voyager receives a distress call and heads towards the coordinates, but finds only remnants of the biomimetic liquid drifting in space. Janeway makes a note of their rescue attempt, and orders the ship to continue on course to home.