Kirk and Spock are delivering medicine to the metal health facility on Elba II. The asylum is home to the most insane criminal of the Federation. Once there, an inmate tells Kirk and Spock that the warden is not who he says he is and before they can do anything, Kirk and Spock are imprisoned with the other criminals.

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.