Earth. The beginnings of our world. In an opening montage, we watch as our primordial planet is terraformed and bioformed by seemingly all-powerful, Godlike alien entities…the ENGINEERS. The seeds of life are introduced to Earth for the first time by these fantastic extra-terrestrials, who have the power to create and manipulate both mechanical and biological matter at will. The montage ends as the earliest genetic recipe for life is sent forth from the Engineers’ massive, towering CITADEL in the dark desert.
The desolate desert of Africa: 2085. The prehistoric ruins of the Engineers’ Citadel is discovered by a corporate construction team tasked with building a nuclear-powered comm-array in the wilderness. Amidst the ancient remains are found highly advanced, biomechanical relics with are determined to be of extra-terrestrial origin. This catches the attention of the mega-conglomerate WEYLAND-YUTANI CORPOTATION, who finances a massive archaeological excavation of the citadel in the hopes of reverse-engineering the alien biotech for financial gain. Running the operation is MEREDITH VICKERS, a cold, calculating corporate executive, who recruits intelligent and independent astrophysicist DR. ELIZABETH SHAW to head up the research team. Assisting Dr. Shaw are xenoarchaeologist DR. THEO ZEDMORE and her fellow astrophysicist DR. LOGAN. Shaw uncovers the secret of the citadel when she discovers a chamber of star charts, which seem to lead the way to the home planet of the Engineers. Also uncovered is evidence suggesting that the Engineers had a database of all life on Earth, and may even have been responsible for its creation including Man.
In a partially-submerged MANHATTAN, Vickers meets with Dr. Shaw and an OPO, (Off-Planet-Officer), CAPTAIN JERAMIAH JANEK, and plans a space mission following the discovered star charts in an effort to find and make first contact with the Engineers. For the scientists and explorers onboard, it will be a journey of discovery, but for Vickers, it’s merely a way of obtaining new technology so that Weyland-Yutani may retain the lead in the competitive race to establish colonies off-world.
The depths of space: 2090. A highly-advanced, top-of-the-line ISRV (Interstellar Research Vessel) PROMETHEUS decelerates as it reaches its target solar system. The vessel’s crew emerges from their cryo-chambers. Along with Elizabeth Shaw, Theo Zedmore, Logan, Meredith Vickers, and Captain Janek, the crew of the Prometheus is comprised of: First Officer MUDOW, Security Officer RAYDEN HOLLOWAY, Navigator CHANCE, Helm Officer RAVEL, Operations Android DAVID 4.0, Political Officer ALDRICH, Medical Officer FRANCIS, Engineer YURI, and Technical Officers SIENA, LETTUP, and TEMBROOK. The crew gets acclimated to their removal from cryo-sleep, their muscles in atrophy from five years without use. Holloway assists Shaw in her physical therapy exercises.
The crew prepares for arrival at the home planet of the Engineers. Shaw and Holloway are instantly attracted to each other, initiating a romantic relationship. However, as they enter the Zeta 2 Reticuli star system, Prometheus encounters a massive disturbance which hadn’t appeared on scanners, one even more powerful than a black hole: a wormhole in space. Prometheus is sucked into the wormhole, and after a harrowing ride, emerges on the other end. The ship crashes on a barren planet, which the damaged computer system identifies as the mission’s final destination.
The crew sets about attempting to repair the Prometheus, while Elizabeth Shaw leads a recon expedition to investigate nearby structures, which turn out to be a cavernous Engineer temple. Inside the temple, Shaw’s team encounters a bizarre BIO-BRAIN, a biomechanical humanoid face set within a towering pillar, as well as thousands of seemingly primitive URNS. David takes several of the urns back to the vessel for analysis.
Investigating the urns, David discovers that they contain the genetic material for thousands of species within a viscous liquid called BIOFORMER which can rewrite any living organism on a cellular level. Basically, possession of the substance gives its owner the power to create life. Vickers interacts with David and seemingly innocently leads to the Bioformer infecting David through a cut in his finger.
Within the depths of the Temple, we find several living Engineers who discover the transgression of the Humans, and remotely rewrite the stolen Bioformer to make it into a weapon. The Engineers capture Holloway and run a number of horrific experiments on him, injecting him with the Bioformer and allowing him to return to the vessel.
Subsequently, the crew of the Prometheus begins to fall victim to the now weaponized substance, as the “carrier” Holloway injects Ravel, Zedmore, Francis, Siena, Lettup, and Tembrook. The victims begin to lose their humanity and slowly transform, experiencing nightmarish visions and hallucinations and making pilgrimages to the depths of the Temple to receive instructions from the Bio-Brain. Holloway, in particular, is resistant to the transformation, fighting against the alien influence with his feelings for Shaw and his responsibilities as security officer. Meanwhile, David finds that the Bioformer is making him into a biological being…making him Human. The crew also finds that their trip through the wormhole took them back hundreds of millions of years and they are actually stranded on primordial Earth, having moved through space and time.
Eventually, as alien influence and the continued lurking presence of the Engineers becomes clear, the crew of the Prometheus turns on each other as the infected human victims fully mutate into PROTOFORMS: vicious, skeletal alien monstrosities which proceed to assault the unaffected Human crew through the halls of the Prometheus.
Mudow, Logan, Chance, Aldrich, Yuri, and Janek end up being destroyed by the Protoforms. In a strange, erotic ceremony, the Protoforms seemingly mate with the Bio-Brain and each other to create thousands of EGGS, the first of a new generation of the monsters. Meredith Vickers is revealed to be a sleeper CONSTRUCT of the Engineers, who are still active in their far future and Shaw’s present due to the time-travelling abilities of the wormhole. Vickers was grown in an Engineer lab but escaped, fleeing to Earth while always wanting to her find creators and take their power. The Engineers activate Vickers’ secondary GENE PROGRAMMING, and she transforms into an ALPHA PROTOFORM: the STAR BEAST.
At last, the two remaining crew members, Elizabeth Shaw and David, seek to confront the Engineers in the Temple. The Godlike entities prove to be utterly evil, and David sacrifices himself as he’s dissolved in the LIFE SEED BIOFORMER which is the basic genetic recipe for MAN: the former android David, it turns out, is the basis for all Mankind. Shaw is captured by Holloway, but he regains enough of his humanity to remotely activate an Engineer vessel for Shaw’s escape, then holds the other Protoforms and Engineers at bay. As Shaw escapes, she finds herself in the midst of the initial Engineer terraforming of Earth which we had witnessed in the opening montage, chased by the former Meredith Vickers who is now the gigantic, horrific Star Beast.
Shaw makes to her escape vessel which blasts off for the wormhole, Holloway fighting the Star Beast with both falling into the wormhole and disappearing. An Engineer PILOT detaches from the Temple in a FAMILIAR VESSEL and follows Shaw, but is lost in the wormhole. Shaw emerges above the Earth of her present day; however, she’s deemed insane and responsible for the loss of her expedition and confined to a psychiatric hospital by the Company. It’s implied that there are at least some of those who believe Shaw’s tale, but have silenced her as part of a cover-up.
In the final scene, we see the vessel of the Engineer that was chasing Elizabeth Shaw emerge from the wormhole in the Zeta 2 Reticuli star system, still in the prehistoric past, and crash on a nearby planetoid, the Engineer Pilot helplessly lost and the EGGS in the ship’s cargo hold stirring as something alive moves from within…