The Federation is attempting to establish relations with the planet, Gideon. Gideon refuses to allow any visitors or sensor scans, but claims to be a complete paradise. After much debate, Kirk and Kirk alone is allowed to beam down. When he materializes, he is still on the Enterprise's transporter pad and the crew is nowhere to be found.

For centuries the alien Krotons have hidden inside their Machine in the Hall of Learning, educating a small settlement of Gonds and selecting the two best students of each graduating class to become their Companions. This is seen as a great honour - until the Doctor and his friends arrive and discover that the Companions are in fact being killed. This revelation rocks Gond society to its foundations, and while the ambitious councillor Eelek seizes the opportunity to stage a coup and grasp power for himself, the Doctor and his friends investigate the Krotons' true agenda. Unfortunately, while doing so the Doctor and Zoe inadvertently wake the Krotons, crystalline conquerors who have been dormant for centuries waiting for the Gonds to become intelligent enough to provide them with the mental energy they need to power their spacecraft. And now that the Doctor and Zoe have arrived, they'll do nicely.