In the ancient past the spaceship of an advanced humanoid alien race arrives in Earth. One of the aliens is left behind and he sacrifices his body to become the first elements of DNA.
In the late 21st century, a star map is discovered by archeologists Elizabeth Shaw and Charlie Holloway, within the archaeological imagery of several otherwise unconnected cultures, including Magdalenian, Mesoamerican and Mesopotamian civilizations. The crew of the vessel Prometheus is sent on a scientific expedition, sponsored by the Weyland Corporation, to follow the map to find the origins of mankind. The crew of the ship is kept in hypersleep, while a single android called David monitors the voyage. The Prometheus finally arrives into its destination, a moon orbiting a gas giant in deep space. The crew of the ship are awakened by David and informed of the missions goals by Shaw and Holloway, under orders by mission director Meredith Vickers. The Prometheus mission is to explore the world of the ancient aliens who left the message in Earth. Shaw informs the crew that the aliens were called "Engineers", since they engineered all living beings. During landing they find what appear to be installations of the Engineers. The Prometheus lands close to one of such installations. Some members of the crew are sent in an expedition using all-terrain vehicles. However, Vickers orders Shaw and Holloway to avoid any direct contact and return if the aliens are found. Janek, the captain of the ship and Vickers monitor the expedition from the Prometheus bridge. The expedition members find a massive building similar to a temple and explore its interior. They find several ampule like artifacts, a giant humanoid head monolith, and also discover the corpses of giant humanoid aliens that are presumed to be the Engineers. A severed head is found by Shaw. Janek and Vickers prompt the expedition members to return to the Prometheus after a sudden gathering storm is detected by the ship's sensors. Botanist Milburn and geologist Fifield get separated from the rest during the rushed return and become stranded in the temple. Shaw takes the Engineer head back to the ship. David takes one of the ampule like artifacts and hides it in a bag without the others noticing. Shaw, Holloway, David and the rest of the crew return to the ship, but just as Shaw and Holloway are about to enter the storms hits them and they are saved from death by David.
Back in the ship Shaw and medic crew member Ford analize the Engineer head with David's help while Vickers observes the procedure. The outer structure of the head is revealed to be a helmet, which is removed revealing a humanoid alien head. A device designed to reanimate and obtain ocular image data from the Engineer head is inserted in it. The head reanimates and explodes shortly afterwards. Vickers confronts David about an order he received from Peter Weyland, the founder and de facto leader of Weyland Corp. David investigates the Engineer ampule and removes and opens a transparent capsule containing a dark substance. He infects Holloway with it under Weyland's orders. The infected Holloway and Shaw have sex.
Back in the temple Fifield and Milburn are attacked by alien snake shaped creatures. Milburn is killed and Fifield falls into a pool of the dark substance from the ampules. Janek, David, Holloway, Shaw, Ford and the crew return to the temple and find Milburn's corpse and one of the creatures inside, which jumps away. David finds what appears to be the bridge of a spaceship inside the temple, with one of the Engineers in hypersleep and a star map with planet Earth on it. Holloway's health worsens and he is rushed back to the ship. Vickers keeps Holloway from entering with a flamethrower. Holloway's pain becomes unbearable and, while Ford holds Shaw, he pleads Vickers to burn him, which she does. Shortly afterwards Shaw develops signs of labor, despite being sterile. She is sedated and taken to the ship's medlab. Shaw awakens and attacks a crew member and Ford when she is told that Peter Weyland ordered them to freeze her to be brought to Earth. Shaw escapes and uses a machine to extract a squid like alien monster from her belly. Peter Weyland is revealed to have been hiding in Vicker's quarters in hypersleep. He has the small tentacled monster locked away by his men in the medlab and explains Shaw that his intention was to obtain the advanced biotechnology of the Engineers to become immortal. Weyland orders another expedition to the temple to awaken the last Engineer. Meanwhile, Fifield's mutated corpse enters the hangar and attacks and kills several crew members. He is ran over by Shaw in a tracked vehicle and finally burned by the crew using flamethrowers. Weyland, David, Shaw, Ford and Weyland's bodyguard travel to the temple and awaken the last Engineer, who promptly severes David's head and throws it at Weyland, killing him. Ford and the bodyguard are thrown to the bridge's walls and killed while Shaw escapes the alien ship, which is revealed by David to be headed to Earth to exterminate the human race. Vickers orders Janek and pilots Ravel and Chance to crash with the alien ship while she uses a escape pod to land near Shaw's location. The Prometheus is destroyed while Janek and the pilots escape in a small craft. Debris from the Prometheus kills Vickers. Janek, and the small craft crew safely land, but they are also killed by the tentacled alien that originated from Shaw, which grew in size and escaped the medlab section, hiding in their ship. Shaw arrives at the small craft while being chased by the last Engineer, who escaped his crashed ship. Inside the small escape craft, Shaw finds the tentacled monster and locks it in the cockpit section of the ship. She is attacked by the Engineer but is saved when she releases the monster which impregnates and kills the alien. Shaw recovers David's remains from the bridge of the crashed alien derelict and uses his knowledge to activate another Engineer ship and travel to the Engineers homeworld to try to stop them using their own biotechnology.