The program for the Emergency Medical Hologram is activated due to what the computer describes as a ship-wide emergency. When the Doctor asks the computer to scan for the crew, he learns that they were all forced to abandon ship. Later, he encounters Torres, who says that she and the Captain stayed behind to stop a warp core breach caused by a Kazon attack; the remaining crew escaped in lifepods. Informed that the injured captain needs his assistance, the Doctor is sent to the Bridge, courtesy of new holo-emitters installed throughout the ship.

After reviving Janeway, the Doctor is summoned to the mess hall to assist Neelix, who is engaged in battle with a Kazon soldier. After the scuffle, the holographic doctor is astonished to learn that he himself is bleeding. When queried, the computer insists that the Doctor is actually Dr. Lewis Zimmerman, the human who created Voyager's EMH. Stranger still, when the Captain tells the computer to shut down all of the ship's holographic systems, Janeway, Neelix, Torres and the Kazon soldier vanish — but the Doctor remains intact.

Just then, Reg Barclay appears and introduces himself as Zimmerman's assistant. Barclay tells the Doctor that he is at Jupiter Station running a holodeck program, but something has gone wrong due to a radiation surge. He claims there's no U.S.S. Voyager lost in the Delta Quadrant; it's simply a program that Zimmerman created. He tells the Doctor that he must end the simulation before radiation from the accident kills him, and the only way to do so is by destroying Voyager.

At first, the Doctor flatly refuses. Yet Reg's arguments are persuasive, and soon the Doctor is prepared to fire his phaser at Voyager's warp core. Suddenly, Chakotay appears and orders the Doctor to lower his weapon, claiming that Barclay is lying.

Chakotay explains that there's been an accident on Voyager that affected the imaging system while the Doctor was in the holodeck. Chakotay says that Barclay himself is a simulation, and that if the Doctor listens to him, he'll wind up destroying his own program. The Doctor isn't sure whom to believe but delays acting on Barclay's advice long enough to prove that Chakotay's story is true. The problem is finally solved, and the Doctor is returned to Sickbay where he reflects on his unusual day.