Kirk and Spock beam down to Elba II to deliver a revolutionary medicine to the insane asylum located there which houses the 15 incorrigible insane criminals of the Federation. Elba II is surrounded by a poisonous atmosphere. Inmate Marta warns Kirk and Spock that their host is not really governor Donald Cory, but they do not believe her. Upon viewing Cory's cell, however, Kirk and Spock discover that the inmate and former starship fleet captain Garth of Isar has imprisoned Cory in his cell and is running the facility with the aid of the other inmates. Garth imprisons Kirk with Cory, and destroys the medicines Kirk and Spock have brought.
Garth is able to change form at will using the technique of cellular metamorphosis (learned on Antos) and attempts to gain control of the Enterprise to escape and punish his former mutinous crew by impersonating Kirk. Garth is thwarted by the password Kirk has arranged with Scotty when Scotty queries ``queen to queen's level 3'' and Garth does not know the proper response to this problem in 3-D chess: ``queen to king's level 1.''
Garth then invites Kirk to dinner with the inmates and Mr. Spock. At the banquet, the green poet inmate Marta recites Shakespeare (which she claims to have written herself) and performs an exotic dance (which Spock find similar to a dance performed by Vulcan school children). We find out that Garth has charted more new worlds than any man in history, but then tried to destroy Antos 4. When Kirk refuses to reveal the counter password, Garth tortures Cory in a specially modified therapeutic chair. When Kirk still refuses, he is strapped in and tortured.
However, Marta convinces Garth to let her try more persuasive techniques. She begins making love to Kirk, then attacks him with a knife. She has arranged for Spock to be freed, and he luckily steps in and nerve pinches her before she can stab Kirk. Kirk and Spock make it to the control room where they contact the Enterprise. However, Kirk smells a rat, and demands that Spock give the countersign instead of himself. Spock, who is actually Garth in disguise, then puts the force field back on and assumes his true form before a security team can be beamed down. Kirk attempts to turn the force field back off, but is stunned by Garth before he can do so.
Garth then holds a ceremony in which he declares himself ruler of the universe, Marta his consort, and Kirk his heir apparent. He then threatens to use a powerful new explosive he has invented on Marta, who is dragged out into the poisonous atmosphere. Garth then carries out his threat, and commands that Spock be brought in. Spock pretends to be knocked out in his cell, then nerve pinches the two guards who have come to fetch him. He makes his way to the control room, where he is confronted by what appear to be two identical Captain Kirks. Spock tries to distinguish the real from the impostor by asking what maneuver was used to defeat the Romulan ship near Tau Ceti. One Kirk correctly gives the maneuver as the Cochrane deceleration, but the other Kirk points out that this is a classic battle maneuver. The two Kirks then have it out, and Spock is able to identify Garth when the real Kirk tells Spock to stun them both in order to assure the safety of the Enterprise. Control of the institution is returned to Cory and Garth and his colleagues are cured using the new drugs.