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Able to travel at speeds far exceeding the speed of light, humans, by the year 2200, are involved in the conquest of deep space.  In United Planets space cruiser C57D, Commander Adams and his all male crew approach the distant star Altair-4 to search for survivors from the spaceship Bellerophon, which landed there twenty years earlier.  Receiving radio contact from the star, Adams soon learns that Dr. Edward Morbius, a philologist on the Bellerophon mission, still remains but insists that he needs no assistance and warns Adams that harm may come to the C57D crew if they interfere.

Adams finally secures landing coordinates and lands the spaceship on Altair-4, a strange, barren land with a green sky and an atmosphere suitable for human life.  Within minutes, a robot named Robby approaches on a gliding transporter and takes Adams, Lieutenant “Doc” Ostrow and Lieutenant Farman to Morbius’ house.  The reclusive Morbius invites them to eat a lunch Robby has “cooked” for them and demonstrates that Robby, his own creation, can insert food in a small aperture, where a built-in chemical lab replicates it to perfection.  Also the house servant and guard, Robby has a built-in safety directive that prevents him from hurting humans.  When asked about the earlier mission, Morbius explains that all others succumbed to a terrible planetary force that ripped them from limb to limb.  Only his wife and he were immune because of their special love of the planet, however, his wife died several months later.

Suddenly, Altaira, Morbius’ daughter, enters, and having never seen any other humans besides her father, is mystified by the men.  Although Morbius realizes that Alta must have more human contact to develop properly, he resists exposing her to the men.  When Adams informs Morbius that he and his crew must remain for ten days to await new orders from earth, Morbius worries that the force will attack again if they remain.

Back at the ship, when Cookie, the cook, secretly asks Robby to help him locate some bourbon, the robot offers to replicate over 60 gallons, causing Cookie to gasp in disbelief and joy.  Meanwhile at the house, after Farman suggests to Alta that kissing might be good for her health, the naïve young woman eagerly submits, but even after several prolonged encounters, she claims to feel no “stimulation.”

Soon after, a frustrated Adams interrupts the flirtation and demands that Alta refrain from wearing promiscuous clothing that tempt his men.  Later that night, an invisible force enters the ship, sabotaging valuable equipment while the crew sleeps.  Soon after, Adams learns from onboard engineer Quinn that they must unship the main drive to get sufficient power to repair the cruiser.  The next morning, as Adams and Doc await Morbius at the house, Adams finds Alta swimming nude in a nearby pool.  She quickly dresses into her new “eye proof” attire, which, despite her attempts to concede to his earlier wishes, still seduces the commander into embracing and kissing her, but the romantic moment is interrupted when Alta’s pet tiger suddenly attacks.  As Adams is forced to disintegrate the beast with his blaster gun, both he and Alta cannot understand the tiger’s sudden change of behavior.

Later, Adams and Doc enter Morbius’ study, where the scientist appears from behind a secret panel and guides the men into a huge network of underground rooms, which Morbius explains, are the remains of an advanced civilization known as the Krels.  Centuries ahead of humans in terms of technological and scientific development, the Krels perished in a catastrophe 2,000 centuries ago, before humans existed.  Once inside the Krel main laboratory, Morbius introduces the men to the "plastic educator," a machine the Krel used to test their mental skills and which Morbius now uses to increase his intelligence in order to understand the Krel’s complex civilization.  Through years of careful study, Morbius has discovered the Krels were devoted to creating a self-maintaining and infinite power source drawing from Altair’s core to free themselves from any "physical instrumentalities.”

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Meanwhile when Cookie leaves the ship to secretly meet with Robby and pick up over 480 pints of bourbon, the monster shorts the ship’s protective fence, enters the craft and kills Quinn, leaving his footprints behind.  Back at the house, after Adams informs Morbius that the United Planetary front must take over the Krel investigation, he learns of the attack by radio and returns to the ship with Doc.  After making a model of the footprints, they assess that creature is a giant biped monster with sloth-like claws.  At first suspecting Robby was involved in the destructive plot, Adams questions Cookie, who gives Robby an alibi by admitting that he was drinking with the robot at the time of the attack.  When Morbius tells Adams that he has a “visualization” of more destruction, Adams suspects the scientist somehow controls the attacks.  That night when radar picks up the invisible monster, the crew fire atomic power weapons, which produce an outline of an enormous roaring beast which kills several men.

Back at the house, Alta, awakened by a nightmare about the monster, rushes into the lab.  As she wakes her sleeping father, dozens of gauges chaotically registering a sudden surge in the power supply slowly quiet while the monster simultaneously halts its attack at the ship.  Later, Doc deduces the monster must be made of nuclear material in order to regenerate and suggests they abandon the mission immediately, but Adams wants to first retrieve Alta and receive an intelligence boost from the plastic educator.  Arriving at the house, Adams envelops Alta in his arms while Doc secretly slips away to the plastic educator.  When Robby returns with the half-conscious Doc in his arms minutes later, the dying man tells Adams that the Krel were very close to living without "physical instrumentation," but forgot about the “monsters from the id.”

After Morbius suddenly appears and calls Adams a fool, Alta finally sees her father’s hatred for the outside world and decides to leave with the commander.  Adams deduces that the Krel’s plan to control the civilization centered around a machine enabling them to create matter anywhere on the planet by mere thought; however, the Krels forgot that their subconscious hate and lust for destruction would also destroy the civilization.  As Morbius retorts that his own mind cannot be creating the monster, they all watch as another invisible beast punctures the house’s shuttered metals walls.  When Morbius orders Robby to kill the beast, the robot malfunctions, unable to harm humans, even the beast created from a human mind.

As the group hides behind the metal door of the underground laboratory, Adams tells Morbius that the plastic educator, far from helping him understand Krel machinery, has made his subconscious able to manipulate it.  He goes on to explain that when Morbius’ twenty comrades voted to return to earth, Morbius’ rage sent a secret “id” to kill them, which will now kill his daughter for defying him.  When Alta begs her father to stop the beast as it melts through the door, Morbius finally admits that Adams’ conclusions must be true and then yells out for the monster to die.  As the raging beast quiets and power gauges shut down, a dying Morbius orders Adams to throw a switch, which sets in motion the irreversible destruction of Altair within 24 hours.

Hours after taking off in their spaceship, Adams, Alta, Robby and the crew watch on a monitor as Altair explodes in a blinding blue light.  With Alta in his arms, Adams predicts that humans will come to develop technology as advanced as that of the Krels and that her father's name will stand like a "beacon in the galaxy" to remind them that they are not “Gods.”