The film opens up on an alien disintegrating and his remains scattering into a waterfall. Then we see Elizabeth Shaw and Charlie Holloway, two archaeologists in the year 2089. They have found star maps in Scotland that match similar maps from unrelated ancient civilizations. There is discussion about whether this might be a clue to find humanity's origin species, the Engineers.
An expedition is then arranged, commissioned by Peter Weyland of Weyland Corporation, to the moon LV-223 on a ship called Prometheus. The crew launches and enters stasis until they reach their destination in 2093. They are instructed not to make contact with the Engineers without permission from their director, Meredith Vickers.
Upon their arrival, the crew discovers a structure with stone cylinders and a humanoid statue inside it and the corpse of a large alien (a la Alien's opening scenes). Afterward, two crew members, Fifield and Millburn attempt to retreat but get lost in the structure. A storm then forces the crew to return back aboard the Prometheus. David is seen stealing a cylinder which leaks liquid. He mixes some of the liquid into the drink and gives it to Holloway, who drinks it before having sex with Shaw in the next scene.
Back in the structure, Fifield is attacked by a different alien, falling into a dark liquid. Millburn is killed and discovered by the crew. David finds an Engineer in stasis, along with a star map like the one in Scotland, highlighting Earth. Holloway flees the scene to reboard the Prometheus, but is forbidden to enter (a la Alien's opening scenes), and begs to be burned to death instead, which Vickers grants. Shaw is discovered to be pregnant, although she was infertile. Shaw uses an automated surgery table to remove the small alien creature from her abdomen (a la Alien).
Weyland, CEO, is then discovered in stasis aboard the ship, and Vickers calls him "Father" in the scene where he outlines his plan to ask the Engineers to prevent his death. After a mutilated and mutated Fifield wreaks havoc, killing several crew members, Janek sheds more light on the structure, hypothesizing that this is the site of a failed weapon, pointing out that there is a spacecraft in the structure. David wakes the Enigeer and tries to explain Weyland's request. The Engineer decapitates David and kills Weyland before boarding. The crew scatters and tries to find ways to escape, trying to get away on the Prometheus. Vickers flees in an escape pod but is crushed by the enemy ship.
Shaw discovers her alien spawn has grown, and then is warned by David's detached head (a la "Ash" from Alien) that the Engineer survived. The Engineer then boards their lifeboat and is killed by Shaw's alien spawn. Afterward, Shaw and David launch another space ship to the Engineer's homeworld seeking to understand why the Engineers were trying to destroy Earth. An alien creature is seen bursting out of the Engineer's chest.