The Federation spaceship Enterprise responds to a distress signal from Camus II, an archaeological exploration site. Among the survivors are Dr. Janice Lester, who once shared an intimate relationship with Captain Kirk, and Dr. Arthur Coleman, the expedition's doctor. Coleman reports that Lester has been exposed to radiation.

Dr. Coleman, Science Officer Spock, and Chief Medical Officer Dr. McCoy attend to other survivors, leaving Lester and Kirk alone. They recall their time at Starfleet Academy and Lester's frustration at not becoming a captain due to Starfleet's ban on female captains. As Kirk investigates an alien device, Lester activates it, immobilizing him. She joins Kirk in the machine, which swaps their souls. The person now appearing as Kirk announces that Janice Lester has assumed Captain Kirk's identity and starts choking the person appearing as Lester.

Spock and McCoy return before "Kirk" can finish, and everyone heads back to the Enterprise. "Kirk" grants Dr. Coleman the full authority to treat "Janice Lester," despite McCoy's objections.

In private, Coleman and "Kirk" discuss their scheme to kill the expedition members, allowing Lester to achieve her dream of commanding a starship.

Spock grows suspicious when "Kirk" orders a course change to Benecia Colony for "Lester's" medical care, despite its inferior facilities and interference with their mission. McCoy orders a medical exam and personality test for the captain.

"Lester" wakes up and seeks help from Spock and McCoy. "Kirk" renders her unconscious again and orders her isolation. Spock interviews "Lester" and becomes convinced of the truth after using his telepathic abilities.

Spock tries to free "Lester" but is stopped by a security team led by the fake Kirk, who accuses Spock of mutiny and orders a court-martial. At the trial, Spock claims Captain Kirk is actually in Dr. Lester's body. "Kirk" counters by accusing Spock of seeking command and offers to drop charges if Spock relents. Spock refuses, causing "Kirk" to lose control.

Disturbed by Kirk's behavior, McCoy and Chief Engineer Scott secretly discuss the possibility of mutiny. "Kirk," having overheard them, declares them, Spock, and "Lester" guilty of mutiny and sentences them to death.

On the bridge, Chekov and Sulu, having witnessed the trial, decide to defy the "captain" and ignore his commands. As "Kirk" loudly accuses them of mutiny, an image of Lester leaves his body but reenters. "Kirk" seeks Coleman's help, who explains that the transfer is reversing and that Kirk must die in Lester's body to prevent it. They head to the brig to poison "Lester," but the reversal completes itself during the struggle. Realizing her triple failure to kill Kirk, eliminate her female gender, and command a starship, Lester suffers a breakdown and pleads with Coleman to kill Kirk. Coleman asks Kirk for permission to care for her. Coleman and Lester are escorted to Sickbay, and the Enterprise continues its mission with Kirk, Spock, and Scotty on the bridge.