Two weeks post the fight at Rigel VII, Captain Pike's vessel detected a space disruption headed their way. It was an old radio alarm "programmed to create disruption and grab attention." The team declared it was dispatched eighteen years prior from the Talos star system, but the first officer revealed that there were no colonies or ships of Earth that far out. Despite having no sign of survivors, Pike refused to explore and instead opted to steer the ship to the Vega colony to give medical aid to the crew's injuries.

Pike requests the Enterprise's chief medical officer, Dr. Boyce, to come to his quarters, but Boyce instead makes a martini for Pike to get him to open up about the battle of Rigel VII. Heavy with the weight of the life-and-death decisions he's had to make, Pike has been considering resigning. However, Boyce advises against it. Spock then interrupts them via the intercom, announcing that a follow-up message from Talos IV confirms that eleven survivors remain. Pike heads to the bridge and orders the ship to Talos at warp speed seven. He is confronted with a beautiful young woman, J.M. Colt, who Number One informs him is his new replacement yeoman. Uncomfortable with having a woman on the bridge, Pike reassures Number One that she is an exception, as she is "different, of course."

Captain Pike and his team travel to Talos IV to discover a band of disheveled male scientists from the collapsed SS Columbia. Lieutenant Jose Tyler explains their advanced technology, which has been impaired by a shattered temporal boundary. Suddenly, a gorgeous young lady comes up to them. She is Vina, born at the same time as the group's crash-landing on the planet. Astonishingly, Vina proclaims Pike is a "prime specimen" while three alien beings with throbbing heads observe through a monitor.

After Boyce shared his medical report with Pike, informing him that the survivors were almost too healthy, Theodore Haskins proposed displaying their "secret," and Vina took Pike away from the rest. Abruptly, Vina, the scientists, and their camp all vanished, and the Talosians overpowered Pike and took him away through a portal in the rock. The landing team attempted to shoot their laser pistols at the door, but their attempts were fruitless. Spock informed the spaceship via his communicator that they had fallen into a trap and lost the captain, inquiring if the ship received his message.

Upon awakening, Pike finds himself in a subterranean chamber with a transparent wall, and he notices a variety of alien beings in the neighboring cells. Talosians then arrive and telepathically communicate their coldly scientific observations about him, concluding that he is sufficiently suited to start "the experiment." Afterward, Pike and Vina relish an imaginary picnic in Mojave.

The Talosians had planned to show Pike illusions rooted in his memories to entice him with Vina. The first illusion transports Pike back to Rigel VII with the mission to save Vina. Pike refuses to cooperate and states that he is not an animal just performing for a meal. Nonetheless, he is keen on gaining knowledge of the illusions and his imprisonment. He successfully navigates through the Kalar's simulated attack and is returned to his cell with Vina.

Vina informs Pike that the Talosians have drastically weakened their planet and themselves by depending on their mental prowess and are now intending to use Captain Pike and Vina as the source for a new, more robust species to repopulate the barren ground. The Talosians administer a punishment to Vina for disclosing this information to Pike.

The Talosians gave Pike a vial of nutrient-rich liquid and demanded he drinks it, even offering to make it look like any food he desired. Rather than comply, Pike decided to go without, which caused the Keeper to punish him with an illusion of being surrounded by scorching fire and threaten even worse punishment if he stayed disobedient. Things seemed to improve when Pike pretended to drink, but he suddenly tried to escape the containment, catching the Keeper off guard. Pike's idea sparked as the Keeper could not read his thoughts during his anger. He asked why, prompting the Keeper to shift the topic to Vina. Once Pike cooled down, the Keeper clarified that she was the only survivor of the Columbia catastrophe. She reaffirmed what she had mentioned: they were being held captive to restart humanity and Talos IV. The conversation ended with Pike still set on escaping and demanding that the Talosians penalize him instead because of his unwillingness, which the Keeper considered an extraordinary progression in their relationship.

Vina takes Pike to a simulated picnic in Mojave, Pike's hometown, hoping to get him to comply. However, Pike remains resolute, knowing the whole scene is merely a trick. Vina comprehends that recreating places familiar to Pike has not been effective, so she guesses an illicit dream might be more successful. The Talosians transform Vina into an exotic Orion slave girl dancer to tempt Pike.

The Enterprise tries and fails to redirect the starship's power to the planet's surface to carve a path for Captain Pike. Spock is then able to locate the Talosians' power generator and plans a mission with two female officers, Number One and Yeoman Colt. To the crew's surprise, their weapons and communicators are not working. Vina is displeased by the presence of the other females, and Number One states that the records suggest Vina is not as young as she appears. Spock orders the Enterprise to leave the area when all rescue attempts are unsuccessful. Still, the Talosians immobilize the ship and search its records, prompting Spock to conclude that the Talosians have no further use for them and will "swat… this fly".

Pike realizes that strong feelings prevent the Talosians from controlling his head and takes advantage of this. As he pretends to sleep, the Talosian magistrate attempts to regain the female officers' lasers out of the cage. Pike grabs the magistrate and disregards the illusions. He figures out that the laser's malfunction is only an illusion and utilizes the laser gun to force the magistrate to stop deceiving him. He now understands that they had destroyed the cage's wall on their first try.

He managed to get away from the Talosians with the women, even though an illusion was created to make it seem otherwise. The door was blasted open, and they made it out, but their communication devices were still not working. Pike offered himself as a prisoner in exchange for their freedom and the Enterprise's. Number One then threatened to blow them all up by overloading her laser pistol in a "force chamber," telling the Talosian magistrate that it was wrong to create an entire race of Humans to be used as slaves.

The magistrate's aides turn up with the summary of the ship's records, which demonstrate that Humans have an "inescapable aversion to captivity," even when conditions are pleasant, rendering them too dangerous for the Talosians' purposes. The magistrate does not apologize for the inconvenience but concedes that their race will become extinct. Pike inquires whether commerce or cooperation might not revive the planet. Still, the magistrate answers that Humans would learn the Talosians' power of illusion and ruin themselves, just as the Talosians did. The crew members are free, but Vina says she cannot go with them. After the others beam them up, the Talosians show Pike Vina's proper form: underneath the Talosian illusions, she is terribly deformed from the crash of the Columbia. They managed to make it so that she could stay alive but could not recover her appearance.

The Talosians accepted the responsibility of caring for Vina, giving her an imaginary Captain Pike to accompany her. Pike returned to the bridge, assuring Dr. Boyce that he was fully invigorated and rebuffing Colt's curiosity about who he would have chosen as a partner.