Harry Kim wakes up on Earth, in 24th Century San Francisco. Harry vividly retains all of his memories of his time aboard Voyager, yet there is no evidence that he was ever on board the ship. His life is entirely different from what he remembers. He now lives in an apartment with his girlfriend, Libby, and works at the shuttlecraft development center at Starfleet Headquarters. He learns that he has designed a new type of runabout, the USS Yellowstone. After he dismisses a meeting with Starfleet Admirals because of "sickness", he looks for any explanation for his current situation. Harry uses his knowledge of Voyager's security codes to obtain classified information about Voyager. Harry realizes that he has somehow swapped places with his good friend Daniel Byrd. While skimming through the crew manifest, Harry notices that Tom Paris is not listed as part of the Voyager crew either. He discovers that Tom Paris now lives a life of crime in Marseilles, France, where he goes to try to enlist Paris' help to figure out what happened, but an altercation with Tom forces him to leave empty-handed.
Upon his return to San Francisco, Harry is apprehended by security and taken to Starfleet Headquarters for questioning concerning his unauthorized access to restricted files using the aforementioned Voyager security codes, as well as his associations with Paris (a former Maquis), and is thought to be a Maquis spy. He is fitted with a security anklet to track his movements, and released. It turns out that a shuttlecraft accident caused Kim to fall into a time-stream and enter a timeline where he was never a part of Voyager's crew. A time-stream alien has been sent to watch over Harry to help guide him through the "transition". He reluctantly gives him information on where the timestream is and tells him that if he recreates the conditions of the accident precisely and flies into the timestream, he might get back to his own reality, but there is considerable risk. Harry tries to tamper with his security anklet, but unfortunately sets off the tampering alarm which alerts Starfleet. Tom Paris comes to Harry's aid and bails him out of a tight situation. They transport to Starfleet Headquarters and steal the USS Yellowstone prototype.
Harry recreates everything he can remember, but when he passes through the coordinates of the timestream, nothing happens. He suddenly remembers that there was also an emergency beam out that was attempted by Captain Janeway before the accident. Harry has Tom transport him off the ship as they hit the timestream, just as the Yellowstone is destroyed in the alternate timeline. Immediately he is returned to his own reality and is happy to find that Tom Paris is also aboard Voyager, and everything is as he remembers it.