The Enterprise has been assigned to search for John Gill, a Federation historian, who disappeared on the planet Ekos some six months earlier. During its approach to the planet, the ship comes under attack from a thermonuclear device that is too advanced to be from Ekos or its neighbouring planet Zeon. The Enterprise easily deals with the threat and assumes a standard orbit around Ekos where Spock tells Kirk that Zeon has a fairly high level of technology but the inhabitants are peaceful whereas the Ekosians are more primitive and anarchic. No contact can be made with Gill so Kirk and Spock beam down to the planet after having subcutaneous transponders inserted by McCoy. These are to be used to locate and retrieve them if they are not heard from within three hours.

Immediately on arrival Spock and Kirk are confronted by a Zeon, who urges them to hide. As they watch, unable to help him for fear of contravening the Prime Directive, he is arrested and taken away by Ekosians wearing Nazi-style swastika armbands. They watch a public viewscreen broadcast and discover that Ekos is at war with Zeon and that the planet is controlled by a military regime run on the same lines as Earth's 20th century Nazi Germany. The broadcast also shows a beautiful, blonde female officer called Daras receiving a medal of honour while a voice announces the beginning of 'a final solution' which will mean the deaths of all Zeons.

The broadcast ends with a salute to the 'Nazi' Fuhrer - John Gill. Kirk and Spock acquire some military uniforms but are arrested before they can locate Gill and are taken to an interrogation centre where they are questioned and tortured. A man they meet there, called Isak, turns out to be the same man they saw being arrested when they arrived. He confirms their fears that the 'Nazi' movement began shortly after Gill's arrival on Ekos. Spock manages to engineer their escape by using the rubindium crystals in their transponders to create a crude laser that burns out the lock on their cell. They find their communicators in pieces that Spock thinks can be repaired, but there is no sign of their phasers.

Isak leads them to his brother, Abrom, who is the leader of a resistance group. Abrom is not keen on helping them until Kirk persuades him that it is their real chance of success. While they talk, Spock repairs one of the communicators but the Enterprise is out of transmission range. The group is arrested in a sudden raid led by Daras, who shoots Abrom. Daras is overpowered and disarmed by Spock and Kirk, who are then told that the 'raid' was only a test of their loyalty and that she is actually a member of the resistance group. The medal they had seen her receive on the tele-broadcast was awarded for denouncing her father to the Gestapo. Her father had planned this in order to get her elevated to a position of trust within the Nazi organisation.

She explains to them that John Gill is only a figurehead who is rarely seen and the real power lies with Deputy Fuhrer Melakon. Gill is due to make a speech from the Chancellery and Daras agrees to help get them past security. They pretend to be a film-crew that is following and shooting propaganda footage of the new heroine Daras. John Gill is eventually located sitting in a broadcasting booth surrounded by guards but he appears to be heavily drugged. Spock contacts the Enterprise and gets McCoy beamed down, dressed as a Gestapo officer, to help them. Although they are stopped and questioned by guards who detected their signal they manage to bluff their way through by pretending to be escorting a 'drunk' McCoy. The doctor confirms that Gill has been drugged and gives him a stimulant to counter the effects.

Meanwhile, Melakon has started the broadcast, announcing the 'final war' with Zeon that Gill is to endorse in his speech. With the help of Spock's mind-meld ability Gill is able to broadcast and starts to denounce Melakon as a traitor. The Deputy Fuhrer grabs a machine gun and fires at the booth to stop him talking, but he is too late as Gill has already told the people that the war must end and orders the fleet to be recalled. Dying, Gill tells Kirk that he knows he was wrong to ignore the Prime Directive but believed the Nazi-style movement would bring order to the planet. His death achieves what his life could not, bringing the Zeons and Ekosians together in peace.