A mysterious woman from an unidentified ship beams aboard the bridge of the Enterprise and renders the crew unconscious. As they begin to revive, Kirk receives an urgent request from McCoy to go to sickbay. He arrives to see Spock's body on a life support machine that McCoy says he can only survive for another twenty-four hours. It appears that their mysterious visitor, Kara, leader of the all-female race of Eymorgs, has removed and taken Spock's brain.

The trail left by the Eymorg vessel is located by Sulu and Chekov, and the Enterprise follows at top speed, ending up in the Sigma Draconis system. Kirk leads a landing party down to the surface of Sigma Draconis VI where it comes under attack by a primitive race of men called the Morg. A series of underground constructions are detected by Chekov, using the ship's sensors, and Kirk and McCoy are beamed down into them accompanied by Spock, whose body has been wired up to a mobile life support system that allows him to walk and follow simple instructions.

The group is soon detected and captured by the Eymorg and taken to Kara who explains that Spock's brain was taken to revive the ailing Controller that oversees the functions of their underground habitat. The Enterprise men manage to escape and reach the room where the Controller is housed. Spock's brain appears to be located inside a large black box that is connected to a control system by translucent rods. They manage to make contact with Spock's consciousness and advise him of what has occurred, enabling him to understand and describe the functions that his brain appears to be controlling.

Kara finds them again and is forced to admit that she performed the surgery on Spock after gaining the necessary knowledge from a machine she calls the Teacher which is a helmet-like device containing the entire stored knowledge of the Eymorg. McCoy risks using the device and manages to obtain the necessary skills and knowledge to reverse the operation. Surgery is immediately arranged and everything goes well until, part way through the operation, McCoy starts to lose the knowledge again and begins to panic at the complexity of what he is trying to achieve. Due to the limited capacity of the human brain it is considered too risky for him to use the Teacher again in such a short space of time.

Spock's vocal chords are re-connected and he is able to assist McCoy by describing what he can feel as the operation progresses. Kirk tells the Eymorg women that they will have to learn to live without their Controller and suggests that they move back to the surface of the planet and resume a more 'normal' relationship with the male Morgs. Aboard the Enterprise, Spock, having recovered fully, goes into a long detailed explanation of the events that have occurred which is all the proof that McCoy needs that he is completely back to normal.