The USS Enterprise, steered by Captain Kirk, comes across a foreign spacecraft from which a mysterious female transmits to the Enterprise's bridge. She renders the whole team unconscious and inspects each of them, taking a particular liking to the Vulcan First Officer Spock. When the crew awakens, Chief Medical Officer Dr. McCoy finds Spock in the infirmary with his brain taken out surgically. Unfortunately, due to his unique Vulcan anatomy, Spock's body can only stay alive in this situation for no more than twenty-four hours. This gives Captain Kirk a limited time to get Spock's stolen brain back.

The Enterprise tracks the ion trail of the alien vessel to the sixth planet of the Sigma Draconis system, a frozen realm amid a glacial epoch. A group of male natives assaults the landing team, and an ensnared aggressor notifies Kirk concerning the "others," who are also known as "the providers of pleasure and anguish." Kirk inquires about their species' female members but needs clarification.

The exploration team is joined by Dr. McCoy and Spock's physical bodies, manipulated by an apparatus McCoy has made. They go far below the ground and stumble upon a woman called Luma. Upon being asked, she reveals a childish mindset. A communicator hears Spock's voice, but Kirk and his crew are caught before their chat can continue. They are then brought to the leader of the women, Kara, the same one seen on the Enterprise bridge. Kirk inquires what they have done with Spock's brain, yet Kara states that she does not comprehend what a brain is, exclaiming, "Brain and brain! What is the brain?" As they try to explain the purpose of a brain, she understands that what they are looking for is the "Controller," on which the underground society is dependent.

The crew who had gone on the mission successfully escaped and followed Spock's signals to a control chamber where his brain had been placed. Kara reveals that the skills needed to extract a brain were given by a mechanism known as the "Teacher," and the knowledge acquired vanishes within three hours. McCoy chooses to use the Teacher himself and quickly starts restoring Spock's brain. Unfortunately, McCoy's ability diminishes before the procedure is done, but Spock helps him complete the process after McCoy re-establishes Spock's power of speech.

Kara is worried that the females may only make it with their leader. However, Kirk promises her that both genders can live on the land together. Spock then begins to tell a lengthy account of the culture of Sigma Draconis VI, making McCoy feel exasperated.