The starship Enterprise reaches the volcanic planet Excalbia to conduct a geological survey when sensors detect carbon-based life on its surface. Surprisingly, an image of Abraham Lincoln appears, and though skeptical of its authenticity, Kirk transports the figure aboard the ship. Lincoln, who seems human and unfamiliar with technology, invites Kirk and Spock to the planet's surface, where Earth-like conditions exist. Despite potential risks, Kirk accepts, believing it is crucial to their mission to make contact with new life forms.

Upon arrival, Kirk and Spock find their equipment missing and encounter Surak, the late father of Vulcan civilization. A rock-like being named Yarnek announces an experiment to determine the stronger human philosophy: good or evil. Kirk, Spock, Lincoln, and Surak represent good, while Colonel Phillip Green, Klingon warlord Kahless, unethical experimenter Zora, and Genghis Khan represent evil. They must fight to the death.

After several skirmishes, Surak dies attempting diplomacy, and Lincoln is killed in a trap. Despite being outnumbered, Kirk and Spock force their opponents to retreat. Yarnek ends the experiment, concluding that good and evil are indistinguishable by their methods. Kirk counters that their motivations, not their methods, define them.

The Excalbians allow Kirk and Spock to return to the Enterprise, leaving the mystery of Lincoln and Surak unsolved. Spock posits that the Excalbians transformed other beings into these historical figures and tapped Kirk and Spock's minds to create their personalities.