Stardate: 48892.1. When the Doctor is activated during a Red Alert, he learns that the ship has been abandoned, and that only B'Elanna Torres and an injured Captain Janeway are left on board. Soon afterwards, Lt. Barclay appears and tells him that his entire time on Voyager is an elaborate simulation, and he's really a holo-engineer by the name of Zimmerman on Jupiter station in the Alpha Quadrant, who has been trapped on a holodeck for six hours. If he does not destroy Voyager's warp core and end the program soon he will die.

Stardate: Unknown. An obsessed Barclay tries to find a way to communicate with the starship Voyager with the use of an artificially generated micro-wormhole. He becomes so involved that he needs the help of Counsellor Troi to keep his grip on reality.

Stardate: Unknown. News reaches Voyager through the up-and-running Pathfinder project that the Doctor's creator, Lewis Zimmerman, is critically ill. In an attempt to save his life, the Doctor's program is transmitted to the Alpha Quadrant, but once there, he finds Zimmerman does not want to be examined by an 'obsolete' EMH program.

Stardate: 54208.3 - The Voyager crew receives a transmission from the Alpha Quadrant that contains an interactive holographic program of Lieutenant Barclay, who informs them that Starfleet has found Voyager a way home.

Stardate: 54732.3 - When the Doctor arranges to have his recently completed holodeck novel published in the Alpha Quadrant, certain aspects of the story hit too close to home among his shipmates.

Stardate: 54973.4 - Twenty-six years in the future, a regretful Admiral Janeway hatches an audacious plan to bring Voyager home sooner, rather than have it spend an additional sixteen years making its journey.