In the 23rd century, a United Planets Cruiser C-57D makes a year-long journey to the distant planet Altair IV to investigate the fate of a colony expedition that landed 20 years prior. Upon arrival, the crew, led by Captain J.J. Adams, makes contact with Dr. Morbius, one of the colony's two survivors. Morbius warns the crew to stay away, citing dangers he refuses to specify, but the ship lands regardless. Greeted by Robby the Robot, an advanced servant created by Morbius, the crew is taken to Morbius’ residence where they meet his daughter Altaira, who is naive about human nature, having never seen any humans other than her father.

Dr. Morbius reveals that he has made an incredible discovery about an extinct advanced race called the Krell, who once inhabited the planet. The Krell left behind a vast underground complex with technology far beyond human understanding, including a machine capable of materializing thought into reality. Despite Morbius’ warnings and demonstrations of the Krell's power, the crew of the C-57D remains on Altair IV, driven by both official orders and personal curiosity. As they stay, they start encountering invisible forces and mysterious threats that jeopardize their lives and mission, forcing them to confront not only the secrets of the lost Krell civilization but also the darker aspects of the human mind.