The Enterprise reaches Sarpeidon, whose sun is about to go supernova. Capt. Kirk, Dr. McCoy, and Spock beam down and meet only one inhabitant, the librarian Mr. Atoz. Knowing the planet's fate, he informs the party that he will soon join his kin. He then shows them the Atavachron, a time-travel device. Suddenly, the female cries out and Kirk runs into the portal, with McCoy and Spock following.

Kirk discovers himself in a world resembling 17th-century England, while McCoy and Spock move back 5,000 years to the ice age of Sarpeidon. They cannot find the portal but can still converse. Spock concludes that the Sarpeidons relocated to the past.

The female offender was shouted at by the officers, who then heard Kirk conversing with his mates and assumed he was a sorcerer. In prison, Kirk brought up the Atavachron to the district attorney. The DA was from the future as well but warned that going back would be hazardous; the journey through time alters the biology of the voyager. Since Kirk was not ready, he could not last more than a few hours. The district attorney brought him to the portal.

McCoy and Spock are rescued by Zarabeth, a female who brings them to a cavern. Spock shows an atypical level of sentimentality, falling in love with Zarabeth and becoming inflamed by McCoy's jibes. Zarabeth is also from Sarpeidon's future but was banished to this era, where she is the only living being. She asserts that Atavachron is a single-direction journey. Spock accepts this, but McCoy charges Zarabeth of lying because she does not want to be deserted. McCoy comprehends that being transported to the past makes Spock regress to the savagery of the old Vulcans. Knowing the emotionality of his actions, Spock asks Zarabeth about the portal once more. She concedes she does not see how a return voyage will affect them.

Despite Kirk's valiant efforts to explain that they were not from Sarpeidon, Atoz continued to attempt to compel them to enter the portal. However, Kirk was able to overpower Atoz and force him to locate McCoy and Spock. Eventually, Kirk was able to engage in conversation with them. Spock is unwilling to leave Zarabeth and is unaware that he would perish if he chose to stay in the past, so he attempts to send McCoy through the portal alone. However, since they had gone through the portal together, they could only return with the other. After they had come back, Atoz dashed into the portal. Spock returned to his usual form and was transported back to the Enterprise.