Captain Kirk, First Officer Spock, and Chief Medical Officer Dr. McCoy are beamed to an Earth-like planet to change the direction of an oncoming asteroid. They come across an obelisk with peculiar symbols and see a village that Spock suggests is inhabited by people descended from Native Americans (Mohican, Navaho, and Delaware). While the other two are not looking, Kirk falls through a trapdoor into the obelisk and is knocked out cold by a beam. Spock and McCoy need help finding Kirk and return to the Federation starship, USS Enterprise, to finish their assignment.

Kirk regains consciousness but has no memory, and Miramanee, a tribal high priestess, and another female witness Kirk's emergence from the "temple." They treat him like a deity and take him to their village, where the tribal leaders require proof of Kirk's godliness. At that moment, an infant is brought in, having drowned. Salish, the medicine chief, announces the youngster as deceased, but Kirk uses mouth-to-mouth resuscitation to restore life. The elders acknowledge Kirk as a god, compelling Salish to hand over his role to Kirk.

Now in charge of the Enterprise, Spock makes it go faster than ever to reach the spot in time to deflect the asteroid. The deflectors, however, only cause a 0.0013 degrees shift in its course, which is not enough to keep it away from the planet. Utilizing the phasers to cut the asteroid like a diamond is unsuccessful, and it further damages the warp drive to the point where Scotty can't fix it. Therefore, the Enterprise returns to the planet on impulse to save Captain Kirk and devise another plan to deal with the rock. It will take 59 days, and Spock remarks that the asteroid will stay four hours behind them the whole way.

Under the tribal custom of the priestess and the medicine chief being wed, Miramanee turns down Salish in favor of Kirk. Despite this, Kirk falls more in love with her and is disturbed by visions of those he feels he truly belongs with during the night. She joyfully informs him that she is pregnant. As the Enterprise draws nearer to the planet, Spock succeeds in figuring out some symbols on the obelisk. It is a device created by 'Preservers' to prevent asteroids from hitting the earth and was used to move endangered humanoids to other places to guarantee their safety. Spock conjectures that the deflector is not working correctly.

As the asteroid draws close to the planet, the sky turns dark, thunder cracks, and powerful gusts of wind start to blow. The elders tell Kirk he must go to the temple to stop the storm. Kirk bangs on the side of the obelisk, desperately trying to get it to open, but the tribe turns on him and Miramanee and begins pelting them with stones. Spock and McCoy appear and startle the villagers, allowing Spock to use a mind meld to get Kirk's memories while McCoy tends to Miramanee's injuries. Kirk can open the trap door in the "temple" by reciting the proper tones, and Spock switches on the deflector just in time. McCoy informs Kirk that Miramanee is beyond saving, and she passes away in his arms as he grieves.