The Enterprise is alerted to a plea for help from a deserted world. When they get there, they are greeted by a telepathic being called Sargon (with the voice of James Doohan), who refers to Kirk and Spock as his "children" and implores them to transport down to the planet. Subsequently, Kirk, Spock, Dr. McCoy, and Lt. Cmdr. Ann Mulhall beam to a secret underground chamber where the voice of Sargon welcomes them from a luminous sphere placed on a stand.

Sargon states that three of them are the remaining individuals of their species; their consciences, preserved in these orbs, have been present here since their world was ruined by conflict. Sargon then exchanges his consciousness into Kirk's flesh and Kirk's awareness into the sphere. Sargon reveals that he and his companions temporarily require human forms to create androids for themselves and then return to his sphere. Kirk, back in his own body, expresses his trust in Sargon.

The crew of the Enterprise, including Captain Kirk, Spock, and Dr. McCoy, meet with Chief Engineer Scott to discuss Sargon's request. After a motivational speech by Kirk, the spheres of Sargon, his wife, and his former enemy are brought up from the planet. McCoy monitors the process as Sargon takes Kirk's body and the other two take Spock's and Mulhall's. Once Sargon and Thalassa become weak from the process, Henoch instructs Nurse Chapel to create a serum that will help the hosts. However, Chapel notices that the serum intended for Kirk is not the right formula, and Henoch admits he plans to kill Kirk and Sargon to keep Spock's body. He then wipes Chapel's memory of the conversation.

The construction of the android vessels commences. Unfortunately, Kirk's health deteriorates faster than the other hosts, necessitating further serum injections. Henoch attempts to persuade Thalassa to remain in the android form since they cannot experience pleasure. She then tries to convince Sargon, but he passes away. McCoy proclaims that Kirk's body has perished, and Sargon is lost. McCoy can revive Kirk's physical state in the sick bay, yet has no way to bring back his mind. Finally, Thalassa offers to reinstate Kirk for McCoy's support to retain Mulhall's body.

McCoy refuses her request, so she retaliates with a telepathic attack; however, she soon changes her heart and stops. The voice of Sargon commends her, and she realizes that Sargon is inhabiting the ship. She then tells McCoy that Sargon has a plan and shuts him out of the examination room before Chapel exits sickbay. When he returns, McCoy discovers that Kirk and Mulhall have been put back into their bodies. Unfortunately, the spheres containing Spock's mind have been destroyed, with Kirk claiming that it was "essential" and requesting McCoy to get a lethal hypospray for Henoch.

Henoch has seized the bridge and is harassing the personnel. He reads McCoy's mind, preventing him from getting the injection. Henoch orders Chapel to use the toxic compound on McCoy, and she appears ready to obey, but ultimately, she injects Henoch instead. Henoch boasts that he can migrate to another body but discovers that Sargon is blocking it. He begs for clemency, but Spock's body falls, seeming dead.

Sargon informs Kirk that he cannot permit this to happen. A luminosity emanates from Spock and Chapel's forms, and Spock returns to life. Sargon clarifies that the injection was not fatal; it was essential for McCoy and Chapel to think it was dead so that Henoch would also believe it. Spock's brain had been briefly put into Chapel's body.

Sargon and Thalassa declared that they would not pursue the construction of physical forms and instead choose to "fade away." They made a final plea, which was granted: to use Kirk and Mulhall's bodies to kiss each other one last time.