Kirk, Spock, and McCoy beam down to a planet about to be destroyed by an asteroid as big as the Earth's Moon which on a collision course. They have 30 minutes to investigate before they must return to the Enterprise and deflect the asteroid.
They beam down in the middle of a pine forest next to a lake, and rightfully wonder at the astronomical chances that another planet should have developed so similarly to Earth. They soon discover an obelisk made of an alien metal which resists sensors and which is inscribed with inscrutable alien writing. And, in yet another amazing coincidence, they also find that the planet is inhabited by a group of American Indians consisting of Navaho, Mohican, and Delaware tribes. When Kirk returns to investigate the alien structure, he accidentally falls inside it while in the process of initiating communicator contact with Scotty. Search parties and sensor scans fail to locate him, and Spock and Scott are forced to leave in order to divert the asteroid and must return for Kirk later.
Inside the alien structure, Kirk's memory is erased and he can no longer remember who he is or what his instruments do. After he finds his way out of the structure, he is discovered by Indians leaving an offering at their ``temple'' and is taken for a god. The Indian elders are somewhat doubtful of the authenticity of Kirk's godhood and ask him to prove it. When a drowned boy is brought before the elders, Kirk practices mouth-to-mouth resuscitation and brings him back to life. Since the boy had been pronounced dead by the medicine man Salish, this is considered sufficient proof, and Salish is force to jealously gives up his medicine badge.
Meanwhile, the Enterprise makes it ways to the deflection point and attempts to push the asteroid off course. However, it suffers from mechanical problems and loses power before it can sufficiently deflect the asteroid.
Salish's jealousy is increased when his betrothed Meramanee (the chief's daughter) tells him she cannot marry him, because she is betrothed to the new medicine man ``Kirok.'' She asks Kirk to set the ``joining day,'' and he, oblivious of the oncoming asteroid, settles on tomorrow. In short order, he gets Mirimani pregnant. He is attacked by Salish, who discovers that he bleeds and therefore cannot be a god. Kirk has also discovers that the secret of the temple has been lost because Salish's father died before passing it along to his son.
Meanwhile, Spock attempts to fragment the asteroid with phasers, but blows out most of Scott's circuits in the process. He then retreats in front of the asteroid, despite Scott's pronouncement that he can do nothing to fix the damage without the help of a Starbase. Spock blames himself for Kirk's marooning and for the failure to destroy the asteroid, and refuses to eat or sleep until he solved the mystery of the obelisk.
On the planet, the winds begin blowing fiercely and the sky to darken. The Indians tell him that he must go to the temple and stop the the natural phenomena before the earth begins to tremble. Kirk finally agrees, but can do nothing since he does not remember how to get inside. In contrast to Kirk's befuddlement, Spock discovers that the symbols on the obelisk are musical notes left behind by a super race known as the Preservers. The preservers passed the the galaxy rescuing primitive cultures in danger of extinction, and the obelisk is a giant astroid deflector.
Meanwhile, Kirk and Meramanee are stoned by the Indians at the temple when Kirk is unable to get inside. McCoy and Spock beam down and frighten the Indians off, but not before Meramanee has been mortally wounded. Spock uses a Vulcan mind fusion on Kirk and manages to restore his memory. When he activates his communicator and says ``Kirk to Enterprise,'' a sliding panel opens up and grants them entry to the obelisk. Inside the ``temple,'' Spock is able to read the symbols and activate the astroid repulsion beam.