Elba II is a planet with a poisonous atmosphere and the site of a Federation penal colony which houses the criminally insane. Kirk and Spock beam down to the colony to meet with Governor Cory and discuss the colony's latest inmate, Garth of Izar. Garth is an ex-captain of a starship and suffered major injuries that were treated by the inhabitants of the planet Antos IV. He subsequently went insane and attempted to destroy them.

Spock and Kirk are taken to Garth's cell where they discover the real Governor Cory has been imprisoned. The 'Cory' they had been speaking to is, in fact, Garth who is now a shape-shifter after his Antosian treatment. He has taken control of the facility, and orders some of his fellow inmates to capture Spock and Kirk. Garth assumes Kirk's shape and contacts the Enterprise, trying to get himself beamed up, but cannot repeat the correct security code necessary to be transported from the planet's surface.

Although Kirk is tortured he refuses to reveal the code word and is only saved when Marta, a green-skinned Orion animal woman and Garth's consort, pleads for his life. Garth needs the Enterprise to enable him to carry out his intention to become 'Lord of the Universe' and considers his options on how to get control of the vessel. Kirk wakes to find himself alone with Marta, who tries to kill him when he rejects her advances, but he is saved by the appearance of Spock.

They make their way to the transporter pads where Kirk is about to give the code word that will allow them to be beamed up but suddenly changes his mind and asks Spock to give the code word instead. 'Spock', of course, cannot give the correct code word because he is really Garth in Spock's form trying to trick Kirk into getting him aboard the Enterprise. Garth arranges a mock coronation for himself to be crowned 'Lord of the Universe' after which he takes Kirk to the colony's control room to see a demonstration of the new explosive that he has invented. Kirk watches the viewscreen in horror as he sees the disloyal Marta blown to pieces by a single grain of the substance.

The real Spock manages to escape from his cell and makes his way to the control room where he is confronted by the sight of two identical Jim Kirks. He cannot decide which one to stun with his phaser until the real Kirk cleverly insists that he stuns them both, putting the safety of the Enterprise before his own personal safety which Garth would never do. A security team is beamed down to recapture the inmates and help restore control of the colony to Governor Cory. Garth is given a course of treatment that leaves him with no memory of his criminal obsessions and restores some measure of sanity to the former hero by helping him to deal with the fact that he is a shape-shifter.