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In 2269 the Enterprise was assigned to investigate the Beta Niobe system, which was soon due to go nova. The single planet, Sarpeidon, had been home to a large civilisation which was now facing destruction from the nova.
On beaming to the surface, Captain Kirk found the planet virtually deserted - only a single individual, a librarian named Mr. Atoz. Atoz declared that the entire population had left, but was unclear as to their destinations. Apparently not realising that Kirk and his officers were not natives, Atoz insisted that they choose a destination for themselves and depart via the "atavachron", a machine located in the library. While investigating this device, Kirk heard a woman screaming and walked through a nearby portal - only to find himself centuries in the past. Accused of being a witch, Kirk was quickly jailed.
Attempting to follow their captain, Spock and McCoy also walked through the portal but in their case they found themselves five thousand years in the past, trapped in a period when Sarpeidon was gripped by an ice age. They made contact with a woman who had also been stranded inthis period, Zarabeth. She had been a political dissident in her own time and had been exiled to the past in order to live the rest of her life completely alone. Spock found himself rapidly becoming more emotional and incapable of using his logic, something which McCoy believed may be a result of his having passed to a time when Vulcans as a whole had not yet embraced logic. Zarabeth claimed that the time portal was one way - if the two Starfleet officers returned to the present, they would die in an instant.
In jail for witchcraft, meanwhile, Kirk befriended a lawyer who had also escaped from this time to Sarpeidon's present. The man helped Kirk to escape from the prison and locate the portal to return to the library.
McCoy refused to believe Zarabeth's story about the time portal, claiming that since he and Spock were not prepared for this time originally then they could indeed safely return. She confessed to being unsure, and McCoy and Spock decided to try to return anyway. They managed to locate the portal and return to the present, and all three officers beamed back to the Enterprise just in time to escape the nova.1