The Enterprise is sent to evacuate a planet's population before a supernova occurs. Kirk, Spock, and Bones beam down to the planet, Sarpedon, to figure out why they can't detect any life forms. On the surface, they find a library run by Mr. Atoz and his clones who tells them that the entire population went back in time to escape the disaster... and then sends Kirk back to a 17th century era where he's taken for a witch, and Spock and McCoy to a frozen wasteland in the distant past.

The TARDIS materialises on a beacon station in deep space moments before space pirates break it up for its argonite. General Hermack of the Space Corps vows to stop the pirates by any means necessary, and when the grizzled old prospector Milo Clancey shows up in a restricted area of space, Hermack concludes that he must be involved in some way. In order to recover the TARDIS from the pirates, the Doctor, Zoe and Jamie must join forces with Clancey as he evades the Space Corps and tries to prove that the real leader of the pirates is the dastardly Maurice Caven. However, this proves more difficult when Caven is revealed to be in league with Clancey's rival, Madeline Issigri - and with her somewhat unwilling help, Caven plans to kill Clancey and his new friends and frame them for the pirate attacks, thus getting away scot-free with his crimes.