Kirk, Spock and McCoy beam down to the planet Triacus in response to a distress call from a scientific expedition led by Professor Starnes but, on arrival, find that all the adult members of the community are dead, apparently having committed suicide by taking cyalodin. During the burial service for the expedition members their children stand and watch, seeming to be strangely unemotional about the event.

The children, who are 'led' by the dead professor's son, Tommy Starnes, are taken aboard the Enterprise where they get together to perform a strange ritual chant. 'Hail, hail, fire and snow, call the angel we will go, far away, for to see, friendly angel come to me'. In answer to this their 'friendly angel' appears, a glowing, richly dressed humanoid being called Gorgan who tells the children to take control of the ship and fly it to the planet Marcos XII where more than a million new 'friends' await them.

Tommy gets permission to visit the bridge and tries to persuade Kirk to take them to Marcos XII but is refused. When Kirk leaves the bridge Tommy concentrates deeply and uses a series of gestures made with his clenched fist to force a telepathic mind control over Sulu and Chekov, making them change the ship's heading towards Marcos XII. Spock advises Kirk of a legend he has found which tells how the planet Triacus was the base for a band of marauders who waged war throughout the entire Epsilon Indi system. The marauders were eventually eliminated after several hundred years but the legend tells how their evil remained behind and only needs some sort of catalyst to bring it alive again.

Attempts to regain control of the Enterprise are punished with telepathic 'revenge' by the children, which results in each affected crewmember having to confront their secret worst fears. Kirk is filled with the fear that he is losing his power of command and Uhura is forced to see herself reflected in a mirror as an ugly, ancient woman. Gorgan, who is an alien being that was brought back to life from a dormant condition when the expedition excavated a cave on Triacus, needs the innocence of the children to help him achieve his ambitions of planetary dominance. He enlisted and retains their obedience by promising them a life without responsibilities or rules.

Spock acquires a recording of the childrens' chant that causes the 'angel' to appear. He plays back the recording to the children, which causes Gorgan to appear on the bridge. Spock then shows the children recordings taken from the expedition showing the happy times that they enjoyed with their parents. When the children start to realise what they have lost the emotional effects on them are very strong and weaken the 'angel's power over them. It rapidly loses its 'beautiful' appearance, showing its true ugliness and eventually decomposes and dies.