Illusion and reality collide for the Doctor.
The Doctor is activated and the computer tells him that there is a ship-wide emergency. He scans the ship for the crew and it turns out that they were all forced to abandon ship. After making his final log, the Doctor goes to deactivate himself, but suddenly Torres enters the room.
Torres explains that the crew had escaped through the lifepods and she and the Captain stayed behind to stop a warp core breach caused by a Kazon attack. Torres says that the Captain is injured on the bridge, and tells the Doctor to go help her. The Doctor now finds out that there are new holo-emitters installed throughout the ship.
After the Doctor helps the Captain, he is summoned to the Mess Hall, where Neelix is under attack from a Kazon. During the struggle the Doctor discovers that he himself is bleeding. He says it's impossible and is astonished to feel pain.
While the Doctor is curing himself of his cut, the computer insists that the Doctor is actually Dr. Lewis Zimmerman, the human who created Voyager's Emergency Medical Hologram. Stranger still, when the Captain tells the computer to shut down all of the ship's holographic systems, the Captain, Neelix, Torres and the Kazon soldier vanish â but the Doctor remains intact.
Shortly after Lt. Barclay, in his first appearance on ST: Voyager, materializes telling the Doctor that he in reality is actually Dr. Zimmerman and that Voyager is not real and that Voyager is really part of a program to test effects of long-term space travel. Lt. Barclay tells the Doctor that the Holodeck is affecting his mind and that radiation is slowly killing him. In order to stop the holodeck and save the Doctor, the Doctor must destroy the ship.
As the Doctor finally believes Barclay and is about to destroy the ship, Chakotay appears, ordering him not to believe anything he has seen. After Chakotay stops him from destroying the ship, it is revealed that the real Voyager ran into an anomaly that caused the doctor's program to malfunction; nothing that happened before Chakotay walked into the holodeck was real. Later, as the doctor recovers in sick bay, "reality" takes another twist, revealing that the doctor is still caught in a simulation. Janeway walks into the holodeck and takes the doctor by the shoulder, bringing him back to true reality.