As a spacecraft departs a planet, a humanoid alien drinks an iridescent liquid and then dissolves. The remains of the alien cascade into a waterfall. The alien's DNA strands mix with the water.

In 2089, archaeologists Elizabeth Shaw and Charlie Holloway discover a star map in Scotland that matches others from several unconnected ancient cultures. They interpret this as an invitation from humanity's forerunners, the "Engineers". Peter Weyland, the elderly CEO of Weyland Corporation, funds an expedition to follow the map to the distant moon LV-223 aboard the scientific vessel Prometheus. The ship's crew travels in stasis while the android David monitors their voyage. Arriving in December 2093, mission-director Meredith Vickers informs them of their mission to find the Engineers and not to make contact without her permission.

The Prometheus lands on the barren, mountainous surface near a large, artificial structure, which a team explores. Inside, they find stone cylinders, a monolithic statue of a humanoid head, and the decapitated corpse of a large alien, thought to be an Engineer; Shaw recovers its head. The crew finds other bodies, leading them to surmise the species is extinct. Crew members Millburn and Fifield grow uncomfortable with the discoveries and attempt to return to Prometheus, but become stranded in the structure when they get lost. The expedition is cut short when a storm forces the crew to return to the ship. David secretly takes a cylinder from the structure, while the remaining cylinders begin leaking a dark liquid. In the ship's lab, the Engineer's DNA is found to match that of humans. David investigates the cylinder and the liquid inside. He intentionally taints a drink with the liquid and gives it to the unsuspecting Holloway, who had stated he would do anything for answers. Shortly after, Shaw and Holloway have sex.

Inside the structure, a snake-like creature kills Millburn and sprays a corrosive fluid that melts Fifield's helmet. Fifield falls face-first into a puddle of dark liquid. When the crew returns, they find Millburn's corpse. David separately discovers a control room containing a surviving Engineer in stasis, and a star map highlighting Earth. Meanwhile, Holloway sickens rapidly. He is rushed back to Prometheus, but Vickers refuses to let him aboard, and at his urging, burns him to death with a flamethrower. Later, a medical scan reveals that Shaw, despite being sterile, is pregnant. Fearing the worst, she uses an automated surgery table to extract a squid-like creature from her abdomen. Shaw then discovers that Weyland has been in stasis aboard Prometheus. He explains that he wants to ask the Engineers to prevent his death from old age. As Weyland prepares to leave for the structure, Vickers addresses him as "Father".

A monstrous, mutated Fifield returns to the Prometheus and kills several crew members before he is killed. The Prometheus' captain, Janek, speculates that the structure was an Engineer military installation that lost control of a virulent biological weapon, the dark liquid. He also determines that the structure houses a spacecraft. Weyland and a team return to the structure, accompanied by Shaw. David wakes the Engineer from stasis and speaks to him in an attempt to explain what Weyland wants. The Engineer responds by decapitating David and killing Weyland and his team, before reactivating the spacecraft. Shaw flees and warns Janek that the Engineer is planning to release the liquid on Earth, convincing him to stop the spacecraft. Janek and the remaining crew sacrifice themselves by ramming the Prometheus into the alien craft, ejecting the lifeboat in the process, while Vickers flees in an escape pod. The Engineer's disabled spacecraft crashes onto the ground, killing Vickers. Shaw goes to the lifeboat and finds her alien offspring is alive and has grown to gigantic size. David's still-active head warns Shaw that the Engineer is pursuing her. The Engineer forces open the lifeboat's airlock and attacks Shaw, who releases her alien offspring onto the Engineer; it thrusts an ovipositor down the Engineer's throat, subduing him. Shaw recovers David's remains, and with his help, launches another Engineer spacecraft. She intends to reach the Engineers' homeworld in an attempt to understand why they wanted to destroy humanity.

In the lifeboat, an alien creature bursts out of the Engineer's chest.

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