In the prehistoric past, a humanoid extraterrestrial known as an Engineer drinks a dark liquid on a barren Earth, causing his DNA to dissolve and seed the planet with the building blocks of human life. In 2089, archaeologists Elizabeth Shaw and Charlie Holloway discover matching star maps painted inside ancient cave ruins across disconnected human civilizations. Interpreting these as an invitation from humanity's creators, the aging billionaire Peter Weyland finances a trillion-dollar deep-space scientific expedition aboard the exploration vessel USCSS Prometheus.
In 2093, the crew arrives at the distant moon LV-223. Mission director Meredith Vickers orders the scientists to avoid direct contact without clearance, while the ship's android, David, monitors operations. The team enters a massive domed pyramid structure, discovering the decapitated corpse of an Engineer and a vast subterranean chamber filled with thousands of urns leaking a mysterious dark biological substance. A severe silica storm forces the team to retreat to the ship, leaving geologist Milburn and cartographer Fifield accidentally stranded inside the alien structure.
David secretly smuggles an intact urn back aboard the ship. Driven by Weyland's hidden agenda to conquer mortality, David spikes Holloway's drink with a drop of the black liquid. Holloway unknowingly impregnates Shaw before succumbing to a rapid, agonizing biological breakdown. When Holloway returns to the pyramid the following morning, Vickers incinerates him with a flamethrower at the ship's entrance to prevent infection. Meanwhile, inside the ruins, a mutated worm creature kills Milburn, and Fifield falls face-first into the mutagenic sludge.
Back in medical quarantine, Shaw discovers she is three months pregnant with a non-human organism despite being infertile. Terrified, she flees to Vickers' automated medical pod, overrides the system, and performs a frantic, conscious emergency caesarean section to cut a writhing, tentacled cephalopod out of her womb. She staples her surgical incision shut and escapes. Fifield returns to the ship mutated into a feral, super-strong monster, killing several crew members before being crushed and burned.
Shaw discovers that Peter Weyland is secretly aboard the ship, clinging to life and hoping the Engineers can cure his mortality. Weyland, David, and Shaw lead a team back to the pyramid, finding a surviving Engineer sleeping inside a stasis hypersleep chamber alongside star charts set for Earth with a cargo of mutagenic bioweapons. David awakens the Engineer and speaks in an ancient proto-Indo-European tongue. The Engineer answers by ripping David's head off and violently beating Weyland to death.
The Engineer activates the spacecraft to launch his genocidal payload toward Earth. Shaw flees, urging ship captain Janek to stop the ship at all costs. Janek and his co-pilots bravely sacrifice themselves, ramming the Prometheus directly into the rising alien vessel. The colossal craft crashes back down, crushing Vickers beneath its hull as it rolls across the plains.
