After being scanned by an unidentified alien ship, the entire crew of the U.S.S. Enterprise, even Data, sustains complete memory loss. Strangely, however, while they have forgotten who they are and what they do, they still possess skills that enable them to operate the ship. All outside communication has been disrupted, but the crew assumes they are in battle due to the remains of a small alien ship located outside.

The crew accesses the ship's computer, which provides them with the name, photo and rank of all personnel responsible for primary operation of the ship. Since learning who they are sparks no memories, no one is surprised when an Executive Officer Commander Keiran MacDuff is listed as second-in-command. Later, Geordi and Data discover information regarding their mission — they have been ordered to cross into Lysian territory and destroy its central command center. The information suggests that the Lysians are responsible for the crew's memory loss. The orders also require the Enterprise to maintain absolute radio silence.

On the Bridge, the crew is uncomfortable with the thought of destroying a small Lysian ship, especially when they discover that the Enterprise is far more powerful than the "enemy" vessel. Picard wants to contact the Federation for verification, but MacDuff insists he cannot, reminding him that their orders state that they are at war with the Lysians and must not contact anyone. Seeing no other choice, Picard fires on and destroys the ship.

Still uneasy, Picard searches for a way to restore the crew's memories. He sends Data and Geordi to access the crew's medical records, but the pair are unable to. They also discover that the mission reports, crew records and personal logs are missing, and are disturbed by the specific nature of the missing information. MacDuff, however, points out that everything that is happening is consistent with their information on the Lysians. Desperate, the crew decides that Dr. Crusher should attempt a dangerous memory-restoring treatment without the benefit of her patients' medical records. MacDuff immediately volunteers for the treatment, during which he appears to suffer a seizure. Afterwards, he tells Dr. Crusher he still remembers nothing.

As Picard prepares to attack the Lysian central command, he learns that the Lysians are so technologically inferior to the Enterprise that they are virtually defenseless. Morally unable to justify the attack, he orders Worf to open the communications channel. MacDuff lunges for tactical control in order to fire on the Lysians, but Riker stuns him with a phaser. The phaser blast reveals that MacDuff is actually an alien. Later, after Dr. Crusher has restored the memories of most of the crew, Picard discovers that MacDuff is a member of a race that has been at war with the Lysians for decades. Although he had the power to manipulate computers and suppress memories, his weapons technology was inferior, so he attempted to use the Enterprise as a puppet.