On an exploratory mission, Kirk, Spock and McCoy beam down from the Enterprise to a beautiful Earth-like planet where they come across a strange alien obelisk. The inhabitants of the planet are akin to native Americans, having been transported to the planet in the far distant past as part of a 'seeding' process carried out by an alien race known only as the 'Preservers'. While examining the obelisk Kirk activates his communicator that causes a trapdoor to open and he falls inside where a ray is projected onto him which erases his memories.

The Enterprise tries to locate and communicate with him without success and are then called away on an urgent mission to attempt to deflect an asteroid that is heading towards the planet on a collision course. Kirk, to the amazement of the local inhabitants, emerges from the obelisk and uses vaguely remembered skills to revive a boy who was thought to have died by drowning, leading them to believe that he is a god. He is given the name Kirok and is made the tribe's medicine man.

In his new position he has replaced the previous medicine man called Salish who doesn't believe that Kirok is a god. He is also angry at his replacement because, according to their traditions, he was due to marry a beautiful tribal princess called Miramanee. Salish challenges Kirok to a fight to prove that he is not a god. Although he loses, he retains his anger and disbelief. The Enterprise fails to deflect the asteroid from its course and the ship returns to the planet while Spock makes further studies of the inscriptions on the alien obelisk and a recording that he has discovered.

Kirk marries Miramanee who soon becomes pregnant but Kirk, although happy with his new life, is still disturbed by dreams of a ship that sails in the sky and cannot shake off the feeling that is where he really belongs. Spock manages to start translating the inscriptions on the obelisk and discovers that it is an asteroid deflector that was left by the Preservers to protect the planet. It is, apparently, not working and their only hope of saving the planet is to be able to make some sort of repair. The approach of the asteroid brings changes to the weather and fierce storms start to hit the planet. As medicine man Kirk is expected to do something about it. He goes to the obelisk but doesn't know how to use its power. Salish picks up on this and works the worried tribe into a frenzy over the lies of the 'false god', urging them to stone him to death.

Spock and McCoy arrive on the planet and locate Kirk, whose memory is restored by a mind-meld with Spock. They discover that the hailing frequencies emitted by their communicators open the trapdoor in the obelisk. They make their way inside to investigate and Spock manages to carry out the necessary repairs and activates the device. The asteroid is successfully deflected and the storms subside but the premature wrath of the tribe has already taken its toll. Miramanee has been fatally injured from the stoning and there is nothing McCoy can do to save her. She and her unborn child die in Kirk's arms with the knowledge that her people, at least, have been saved.