Negotiations between the United Federation of Planets and the Klingon Empire have collapsed. As a result, the USS Enterprise is sent to the world of Organia, a non-aligned planet near the Klingon border, to prevent the Klingons from taking advantage of its strategic location. However, as the Enterprise approaches Organia, the ship is attacked and destroys a Klingon vessel.

When Kirk and Spock landed on the planet, they noticed a serene, though less-developed, town. Kirk asked Ayelborne, the mayor, for the Federation's support to fight the Klingons, but the Organians vehemently disagreed with any violence. After the Klingon armada showed up in the sky, Kirk commanded the Enterprise to depart, leaving himself and Spock in the world below.

To elude suspicion, Ayelborne transforms Kirk and Spock's appearances, and the Klingons take possession of the planet without challenge, appointing the highest-ranking Klingon, Kor, as the military ruler. Kor uses a "mind sifter" to ensure Spock is not a spy and names Kirk as the Organian representative to the occupied forces. Spock employs his mental capabilities to stand up to the test of the machine.

That night, Spock and Kirk attempted to motivate the Organians by sabotaging an arms depot close to the town. When Ayelborne uncovered the Starfleet officers' true identities to Kor, the council surprisingly liberated them before the Klingons could extract information from them by torture. As Kirk and Spock struggled to understand the council's peculiar behavior, Kor commanded the execution of two hundred Organians, yet the council was unaffected.

As the Federation's forces and the Klingon armada prepared for a battle in the system, Captain Kirk and Spock infiltrated the Klingon base to stir the locals to rebellion. They took Kor prisoner and were set to make a last stand. Then, the Organians revealed their proper form as highly advanced incorporeal creatures. They immediately immobilized both sides, obliging them to cease their fighting. The Organians prognosticated that the two sides would cooperate in the future.