Stardate 5423.4: The Enterprise arrives in orbit above the plant Gideon. Gideon isn't a Federation member and Kirk has been sent to negotiate a treaty. Gideon has refused sensor scans or a delegation, but finally agrees to meet with just Kirk. Uhura relays the coordinates provide by the Gideon council for transport. Kirk dematerializes… and finds himself back on the transporter pad. Believing he wasn't transported, Kirk wonders why Spock left and tries to raise the first officer on the intercom. He gets no response, from Spock… or anyone else. Kirk goes through the ship to the bridge and finds no one aboard, although the Enterprise is still in orbit above Gideon.
Kirk searches the entire ship and finds nothing. He does notice a brief memory loss during which he suffered a bruise on his arm.
On the Enterprise, Uhura relays a message from Ambassador Hodin and the Gideon Council to Spock. Hodin asks when Kirk will be arriving and reports that he never arrived. Hodin confirms the coordinates and asserts that Spock must have messed something up. Spock requests permission to beam down and conduct a search but Hodin refuses, standing on his planet's insistence on avoiding contact with outsiders. McCoy insists that they ignore Hodin but Spock stands by a diplomatic solution for the time being. Spock sends a message to Starfleet requesting permission to take any means necessary to find the captain, and orders a scan of space.
Kirk finds a girl literally dancing with joy down the hallways. She identifies herself as Odona and asks why Kirk brought her there. She doesn't know who brought her there and her last memory is of an auditorium almost entirely filled with thousands of people. Kirk goes to check things out.
While Spock tries to get an answer from the Federation bureaucracy, Kirk realizes that nine minutes have disappeared when he beamed up. Odona has no memory of the planet Gideon and when Kirk switches on the view screen, he discovers they have left orbit and are in an unfamiliar sector of space.
Hodin contacts Spock to pass on the good news that they have searched for Kirk and found no presence of him on Gideon. Spock isn't impressed and diplomatically notes that Hodin may have misunderstood his request. Hodin suggests he be clearer and Spock is forced to apologize for the "noise" of the crew protesting. Hodin refuses Spock's request to beam down but Scotty disputes the claim that the transporter malfunctioned. Hodin reluctantly allows Spock to test the equipment but only by beaming up a council member after they restate the coordinates. Scotty beams up the council member, confirming the transporter is working. However, Hodin refuses to let anyone beam down and signs off, and Spock sends another request to Starfleet.
Kirk brings the ship out of warp, according to the sensors. Odona asks Kirk to make the current situation last forever, and Kirk determines they have enough supplies to last forever. Kirk tries to get Odona to remember why her people wish to be alone, and she notes that they never can be, and that they would kill because there are so many of them. Kirk wonders if she has been sent to kill him, or to die. They kiss, unaware that dozens of faces are watching them from the view screen
Kirk goes to look for a medical kit to cure his bruise, and Odona wonders if he'll grow sick and die from it eventually. They're interrupted when they hear a loud pulsing noise that Kirk doesn't recognize. Suspecting a storm, they go to a viewing port and they see dozens of individuals outside all looking in for a moment, until the image turns back into a starfield. The sound stops and Kirk believes it's the heartbeat of thousands of people pressing against the ship. Kirk wonders if it's a mirage or illusion, and believes whoever is behind the situation is trying to make them content with the situation so they'll say. Kirk demands answers from Odona, who seemingly knows nothing. They're unaware that Ambassador Hodin is watching them from the council chambers.
Odona starts to grow ill, despite saying that there's never been sickness or death on her planet. She collapses and as Kirk takes her to Sickbay, Hodin and the others intercept him and say their experiment has passed the first stage. Hodin says he is grateful that Kirk helped make Odona ill and takes her, then orders his men to guard the captain, saying they'll need him for a long time.
Spock finally contacts Admiral Fitzpatrick and asserts he knows where the captain is being held, although it is not in the Gideon council chamber where he supposedly beamed down. However, Spock has no evidence that the captain's life is in danger and Fitzgerald refuses his request.
Hodin assures his daughter, Odona, that her suffering will be great and she describes her pain. Kirk demands to see her and Hodin informs her that they've infected her with Vegan choriomeningitis, a disease Kirk almost died from. They took a blood sample from him and need it to make Odona die.
Spock decides to disobey Starfleet orders and replays the initial coordinates and compares them to those given to Scott to beam up the council member. There's a one-digit discrepancy and Spock beams down to the original coordinates. He materializes on the fake Enterprise transporter platform and tries to contact the captain.
Kirk is taken to the council chamber confronts Hodin who explains that their planet once was a paradise and the planet was germ free. However, the Gideon natives gained the ability of cellular regeneration, becoming practically immortal. The birth rate rose and the people of Gideon believe all life is sacred, and so refuse any intervention in the birth process. Kirk refuses to participate but Hodin and the others need his blood to create the virus to adjust the Gideon life cycle.
Spock contacts the real Enterprise and informs them of the situation, then goes to find the captain. Hodin gets word that Odona is delirious and is calling for Kirk, who is allowed to see her. Kirk insists they can cure her but Hodin insists her death will serve as a symbol to inspire others to volunteer for death. Odona is still brave in the face of death and intent on sacrificing herself for her people.
Spock renders Kirk's guards unconscious and calls for beam up as Kirk leaves with Odona. They get her to Sickbay and McCoy cures her, and she admits she deceived him. Kirk suggests she leave but Odona insists on staying with her people so that she can provide the blood that will act as a serum for those who choose to die. Odona wishes that Kirk might stay but they both have their duty, and he escorts her to the transporter room.