The Enterprise receives a distress call from a planet hundreds of light years too distant to have been visited by any Earth ship. Spock determines that the planet is similar to Earth, but older, and also that its atmosphere was ripped away a half million years ago. Spock also detects no sign of life. As the Enterprise nears the planet, a voice identifying itself as Sargon asks Kirk to assume a standard orbit about the planet. The voice also addresses the crew of the Enterprise as ``my children.'' Spock detects a power source originating 100 miles below the planet's surface, and Kirk and McCoy prepare to beam down. Kirk wants Spock to stay on board, but the Enterprise loses all power when he states this. When Kirk changes his mind and proposes to bring Spock along, all power comes back on. Astrobiologist Dr. Anne Mullhall also tags along, claiming she has received an order to accompany them despite the fact that Kirk has given no such order. Strangely, the security guards get left behind when the transporter is activated. Furthermore, after arriving, the communicators function through 100 miles of rock despite the fact that they should not.
The landing party discovers evidence of an ancient culture on a planet whose habitable surface was destroyed long ago by a self-inflicted cataclysm. Sargon is revealed as a spherical receptacle containing pure energy which is the ``essence'' of Sargon. Sargon reports that his people colonized the galaxies 6000 centuries ago, and that humans and Vulcans may be their descendants. When Kirk asks Sargon how he can help, Sargon occupies Kirk's body. This transference produces great stress on Kirk's body, causing McCoy to become alarmed. Sargon then asks to borrow the bodies of Spock and Anne Mullhall for the surviving minds of Filisa (his wife) and Hanoc (a member of the opposing side in the great war), the only other two survivors, so that they may construct androids. Kirk, Spock, and Mullhall voluntarily agree, and the receptacles are beamed aboard the Enterprise for transference.
As before, the stress is too great on the human bodies, although Spock's body proves to be rugged enough to sustain Hanoc temporarily. Sargon leaves Hanoc in charge of formulating a metabolism depressant, but Hanoc takes the opportunity to doctor the formula to kill Sargon (and Kirk) so that he can stay in Spock's body. Nurse Chapel notices that the formula is incorrect, but Hanoc erases her memory and she forgets noticing this. While he is possessed by Hanoc, Spock flashes uncharacteristic smiles on several occasions.
Hanoc finds that Felissa is also desirous of keeping her body and does not wish to return to her receptacle. Meanwhile, Sargon is feeling the effects of the incorrect serum, and even Dr. McCoy cannot save him from dying in Kirk's body. Felissa attempts to engage McCoy in her scheme to remain in Mullhall's body while pretending to have left it, but then relents.
Sargon, who reveals himself to still be alive, expresses his approval. He and Felissa now scheme to force Hanoc to leave Spock's body. They restore Kirk to perfect health, but destroy the receptacle containing Spock's consciousness in order (to prevent Hanoc from returning to it) and attempt to administer a deadly poison. Hanoc has taken control of the ship, but Nurse Chapel manages to inject him. It turns out that Sargon has been sharing consciousness with Nurse Chapel, and that the hypo had actually only contained a tranquillizer. Spock is therefore returned to perfect health, but Hanoc, who had fled Spock's body believing it to have been poisoned, is now destroyed. Sargon realizes that the temptation for he and Filissa to abuse their god-like powers is too great, and he and Filissa desert their bodies and fade into oblivion.