As a hovering spacecraft departs, a humanoid alien drinks a dark bubbling liquid, and then starts to disintegrate. As its bodily remains cascade into a waterfall, the alien’s DNA triggers a biogenetic reaction.
In 2089, archaeologists Elizabeth Shaw and Charlie Holloway discover a star map among several unconnected ancient cultures. They interpret this as an invitation from humanity’s forerunners, or “Engineers”. Peter Weyland, the elderly CEO of Weyland Corporation, funds the creation of the scientific vessel Prometheus to follow the map to the distant moon LV-223, orbiting a ringed planet, in the Zeta Reticuli star system. The ship’s crew travels in stasis while the android David monitors their voyage and studies linguistics such as Schleicher’s fable. Arriving in 2093, they are informed of their mission to find the Engineers. Mission director Meredith Vickers orders them to avoid making contact without her permission. The Prometheus lands near a large artificial structure, which a team explores.
Inside they find numerous stone cylinders, a monolithic statue of a humanoid head, and the corpse of a large alien, thought to be an Engineer. They find other bodies and presume the species is extinct. David secretly takes a cylinder, while the remaining cylinders begin leaking dark liquid. A rapidly approaching storm forces the crew to return to Prometheus, leaving crew members Millburn and Fifield stranded in the structure. In the ship, the Engineer’s DNA is found to match that of humans. Meanwhile, David investigates the cylinder and discovers a dark liquid. He intentionally infects Holloway with the substance. Shaw and the unknowingly infected Holloway later have sex.
Inside the structure, a snake-like creature kills Millburn, and it sprays a corrosive fluid that melts Fifield’s helmet, exposing him to the leaking dark liquid. The crew later returns to the structure and finds Millburn’s corpse. David separately discovers a control room containing a surviving Engineer in stasis, and a star map highlighting Earth. Holloway’s infection rapidly ravages his body, and he is rushed back to Prometheus. 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 with an alien offspring. Shaw uses an automated surgery table to cut it out. Weyland is revealed to have been in stasis aboard Prometheus, and explains to Shaw he wants to ask the Engineers to prevent his death from old age. As Weyland prepares to leave for the structure, Vickers calls him “Father”.