In a bizarre area that is outside of space and time, the Enterprise systems fail; even the life-support systems break down, imperiling the crew. A satyr-like creature appears on the bridge, calling himself Lucien. He restores the ship's power, then transports Kirk, Spock, and McCoy to the arid surface of the world. He seems to use magic to restore Kirk, whose body has lost its integrity and become a wavering mirage. Lucien transports them again, claiming to change the world of Megas-Tu to something they can understand.

Lucien tells them of Megas-Tu's magical history, and reveals that some of the practitioners visited Earth long ago. Suddenly spooked, Lucien sends the trio back to the bridge of Enterprise, warning them not to allow themselves to be discovered. Spock practices, and is soon able to harness some of the magical power of the area. As Sulu does the same, Kirk theorizes that belief in magic is as potent a force as energy and matter are in the natural universe.

When the Enterprise crew is detected, the vengeful spirits of Megas-Tu decide that the humans must suffer. They draw the ship to the surface of the planet, and split it in two parts. The crew find themselves in stocks, trapped in a representation of Salem, Massachusetts circa 1691, where they find out that the Megans who visited Earth had been harshly treated ... and eventually burned as witches at the Salem Witch Trials!

As a non-human, Spock defends the crew at their trial, calling on Lucien and Kirk, to speak. The captain quotes General Order #1, and Earth's history since the days of Salem. The Megans release the Enterprise crew, but decide to impose exile on Lucien. Kirk challenges the prosecutor, Asmodeus, to a duel for Lucien's freedom, and his compassion proves that the people of Earth have indeed changed. The Enterprise and its crew are allowed to leave, secure in the knowledge that the Megans will now no longer fear or distrust humanity.