In the 23rd century, the United Planets starship C-57D reaches the distant planet Altair IV to determine the fate of an expedition sent there 20 years ago. Dr. Edward Morbius, one of the earlier expedition's scientists, warns the ship not to land because he cannot guarantee their safety, but Commander John J. Adams ignores the warning and lands.
Adams and Lieutenants Jerry Farman and "Doc" Ostrow are met by Robby the Robot, who transports them to Morbius' residence. Morbius describes how all other members of the expedition had been killed one by one, by a "planetary force" and how their starship had been vaporised as the last survivors tried to leave in it. Only Morbius, his wife (who later died of natural causes) and their daughter Altaira were somehow immune. Morbius offers to help the newcomers leave for home, but Adams says he can’t without further instructions from Earth.
The next day, Adams finds Farman kissing Altaira; furious, he dresses down Farman and criticises Altaira for being naive and wearing clothes that make her sexually attractive to men. That night, an invisible intruder sabotages some equipment on the starship. The next morning, Adams and Ostrow go to Morbius’ residence to discuss this. While waiting for him, Adams apologies to Altaira for his behavior and they kiss. They are attacked by Altaira's pet tiger; Adams disintegrates it with his blaster.
Morbius appears and tells Adams and Ostrow that he has been studying artefacts of the Krell (an advanced race that perished overnight 200,000 years ago). One is a device that enhances the intellect, which Morbius had used. He barely survived, but his intellectual capacity had doubled. Another is a 20 miles (32 km) square underground machine, still functioning, powered by 9,200 thermonuclear reactors. Adams tells Morbius to share his discoveries with Earth. Morbius refuses, saying "humanity is not yet ready to receive such limitless power".
Adams erects a force field fence around the starship but the intruder eludes it and murders Chief Engineer Quinn. Morbius warns Adams he has a premonition of further deadly attacks. That night, the invisible intruder returns, but is outlined in the force field. Blasters don’t hurt it. The creature kills Farman and two other crew. When Morbius is awakened by Altaira's screams, the creature vanishes.
Adams tries to persuade Altaira to leave; Ostrow sneaks away to use the Krell intellect enhancer; he is fatally injured, but before dying tells Adams that the Krell machine can create whatever one wants by thought alone, but that the Krell had forgotten this could include "monsters from the Id". The machine gave the Krell’s subconscious desires free rein and unlimited power: this had caused their extinction. Adams concludes that Morbius's subconscious mind must have made the machine create the creature that both killed the original expedition members and attacked his crew. Morbius refuses to believe him.
Altaira tells Morbius she will leave with Adams. Robby detects the creature approaching them. Morbius commands Robby to kill it but the robot shuts down instead. Adams, Morbius and Altaira hide in the Krell lab, but the creature melts its way through the doors. Morbius accepts the truth, confronts and disowns his other self, and the monster vanishes, but Morbius is fatally injured. Before he dies, he has Adams activate a planetary self-destruct device and arrange to escape in time. At a safe distance, Adams, Altaira, Robby and the surviving crew watch the destruction of Altair IV. Adams reassures Altaira that in about a million years, the human race will reach up to where the Krell were and it will remind them that they are, after all, not God. They embrace as the ship departs to return to Earth.