Harry Kim is aboard a shuttlecraft as it is shaking violently. As he contacts Voyager, Captain Janeway attempts to beam him out, and he finds himself awakening on Earth in San Francisco next to his girlfriend, Libby, whom he had dearly missed. The date is exactly the same as he remembered, but his life is completely different: Harry vividly retains all of his memories of his time on Voyager, yet there is no evidence he was ever aboard. Kim finds he had been denied a posting on Voyager and then took an assignment working at the shuttlecraft development center at Starfleet Headquarters, learning that he has designed a new type of runabout, the prototype named USS Yellowstone.
After he leaves a briefing with staff 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 on his ship. Kim realizes he has somehow swapped places with his good friend Daniel Byrd. While skimming through the crew manifest, Kim notices Tom Paris is not listed as part of Voyager's crew either. He learns Paris now lives in Marseilles, France after his parole, and goes there to try to enlist Paris' help in figuring out what happened. An altercation with Paris at a pool hall there forces him to leave without his friend's assistance. Nevertheless, Paris does tell Kim that he'd lost his "advisor's" spot on Voyager after DS9's ill-tempered shapeshifting security chief threw him in the brig for having gotten into a fight with a Ferengi on the station prior to Voyager's departure. (This altercation almost happened between Quark and Kim in the pilot, but Paris had intervened.)
Upon his return to San Francisco, Kim is apprehended by security and taken to Starfleet Headquarters for questioning concerning his unauthorized access to restricted files using the Voyager's security codes, as well as his recent association with Paris (a former Maquis). Kim finds himself suspected of being a Maquis spy and is fitted with a security anklet to track his movements and released. It turns out 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 sets off the tampering alarm which alerts Starfleet. Paris comes to Kim's aid and bails him out of a tight situation. They transport to Starfleet Headquarters and steal the Yellowstone.
Kim recreates everything he can remember, but when he passes through the coordinates of the timestream, nothing happens. He suddenly remembers there was also an emergency beamout attempted by Captain Janeway before the accident. Kim has Paris transport him off the ship as they hit the timestream, just as Yellowstone is destroyed in the alternate timeline. Immediately he is returned to his own reality and is happy to find Paris is also aboard, and everything is as he remembers it.