In the 23rd century, Starship C-57D reaches the distant planet Altair IV to determine the fate of a 20-year-old expedition. Dr. Edward Morbius (Walter Pidgeon), one of the expedition's scientists, contacts the Earth ship. He states no assistance is required, warning the starship not to land; he cannot guarantee their safety. Commander John Adams (Leslie Nielsen) insists on landing co-ordinates.
Adams, Lieutenant Jerry Farman (Jack Kelly), and Lieutenant "Doc" Ostrow (Warren Stevens) are met by Robby the Robot, who transports them to Morbius' residence. There, Morbius claims that an unknown "planetary force" killed nearly everyone and finally vaporized their starship, the Bellerophon, as the last survivors tried to lift off. Only Morbius, his wife (who later died of natural causes) and their daughter Altaira (Anne Francis) were somehow immune. Morbius fears that the Earthmen are in danger, and (silently) that Altaira is intrigued by them.
The next day, Adams finds Farman educating Altaira on kissing; furious, he dismisses Farman and berates Altaira for her naivety and revealing clothes. Altaira is frustrated, but designs a new, more conservative dress to please Adams. That night, an invisible intruder sabotages equipment aboard the starship. Adams and Ostrow go to confront Morbius the following morning. Waiting for Morbius to exit his study, Adams steps outside, only to encounter Altaira wearing her new dress. Adams sincerely apologizes and Altaira notes that she tailored her dress for him. Realizing mutual affection, they kiss.
Upon Morbius' appearance, Adams and Ostrow learn he has been studying the Krell, a highly advanced native race that mysteriously died out suddenly 200,000 years before. In a Krell laboratory Morbius shows them the "plastic educator", a device capable of measuring and enhancing intellectual capacity. When Morbius first used it, he barely survived, but discovered his intellect had been permanently doubled. This enabled him to build Robby and the other "technological marvels" of his home with information obtained from a Krell library. Morbius then takes them on a tour of a vast cube-shaped underground Krell machine complex, still functioning and powered in tandem by 9,200 thermonuclear reactors. Afterwards, Adams demands that Morbius turn over his discovery for Earth supervision. Morbius refuses, citing the danger that Krell technology would pose to humanity if he were to do so prematurely.
In response to the sabotage, Adams orders a force field fence deployed around the starship. This proves useless when the intruder returns and murders Chief Engineer Quinn (Richard Anderson) undetected. The starship's crew later discover it is invisible, only becoming visible when outlined by the fence's energized force field and fire from the crew's weapons. The weapons have no effect, and it kills Farman and two others. Morbius, asleep in the Krell lab, is startled awake by screams from Altaira; at the same instant, the roaring creature vanishes.
Later, while Adams confronts Morbius at his home, Ostrow sneaks away to use the Krell educator; as Morbius had warned, he is fatally injured. Ostrow explains to Adams that the Great Machine was built to materialize anything the Krell could imagine. With his dying breath, he says the Krell forgot one thing: "Monsters from the Id." Adams asserts that Morbius' subconscious created the monster that killed the members of the original expedition and attacked his crew. Morbius refuses to accept this.
After Altaira and Adams declare their love to Morbius, Robby detects the creature approaching. Morbius commands the robot to kill it, but Robby knows it is a manifestation of Morbius; his programming to never harm humans forces Robby to shut down. The monster melts through the almost indestructible Krell metal doors of the laboratory where Adams, Altaira and Morbius have taken refuge. Morbius finally accepts the truth: the creature is "his evil self". He confronts and disowns the creature as it enters, but is fatally injured. The monster then disappears. Before Morbius dies, he has Adams initiate an irreversible chain reaction within the Great Machine. He then warns that Adams and Altaira must be 100 million miles away within 24 hours. From deep space, Adams, Altaira, Robby and the surviving crew witness the destruction of Altair IV.
Who does Altaira aim to please in tailoring her new dress?
Adams