The central theme in Prometheus concerns the eponymous Titan of Greek mythology who defies the gods and gifts humanity with fire, for which he is subjected to eternal punishment. The gods want to limit their creations in case they attempt to usurp the gods. The film deals with humanity's relationship with the gods—their creators—and the consequence of defying them. A human expedition intends to find God and receive knowledge about belief, immortality and death. They find superior beings who appear god-like in comparison to humanity, and the Prometheus crew suffer consequences for their pursuit. Shaw is directly responsible for the events of the plot because she wants her religious beliefs affirmed, and believes she is entitled to answers from God; her questions remain unanswered and she is punished for her hubris. The film offers similar resolution, providing items of information but leaving the connections and conclusions to the audience, potentially leaving the question unanswered. Further religious allusions are implied by the Engineers' decision to punish humanity with destruction 2,000 years before the events of the film. Scott suggested that an Engineer was sent to Earth to stop humanity's increasing aggression, but was crucified, implying it was Jesus Christ. However, Scott felt that an explicit connection in the film would be "a little too on the nose."
Artificial intelligence, a unifying theme throughout Scott's career as a director, is particularly evident in Prometheus, primarily through the android David. David, the android, is like humans but does not want to be like them, eschewing a common theme in "robotic storytelling" such as Blade Runner. David is created in the image of humanity, and while the human crew of the Prometheus ship searches for their creators expecting answers, David exists among his human creators yet is underwhelmed; he questions his creators about why they are seeking their own. Lindelof described the ship as a prison for David. At the conclusion of the film, David's creator (Weyland) is dead and his fundamental programming will end without someone to serve. Lindelof explained that David's programming becomes unclear and that he could be programmed by Shaw or his own sense of curiosity. Following Weyland's death, David is left with Shaw, and is sincere and interested in following her, partly out of survival and partly out of curiosity.
Another theme is creation and the question of "Who Am I? Who Made Me? Why Hast Thou Forsaken Me?" Development of the in-universe mythology explored the Judeo-Christian creation of man, but Scott was interested in Greco-Roman and Aztec creation myths about gods who create man in their own image by sacrificing a piece of themselves. This creation is shown in the film's opening in which an Engineer sacrifices itself after consuming the dark liquid, acting as a "gardener in space" to bring life to a world. One of their expeditions creates humanity, who create artificial life (David) in their own image. David then introduces the dark liquid to Holloway who impregnates a sterile Shaw, and the resulting child impregnates an Engineer, creating the child of all three generations. Scott likened the Engineers to the dark angels of John Milton's Paradise Lost, and said that humanity was their offspring and not God's.
Shaw is the only religious believer in the crew and openly displays her religious belief with a necklace of a Christian cross. Lindelof said that with her scientific knowledge, her beliefs felt outdated in 2093. Shaw is excited when she learns that she was created by the Engineers and not a supernatural deity, but it does not cause her to lose her faith, it reinforces it. Lindelof said that asking questions and searching for meaning is the point of being alive, and so the audience is left to question whether Shaw was protected by God because of her faith. Scott wanted the film to end with Shaw's declaration that she is still searching for definitive answers. In addition to the religious themes, Lindelof said that Prometheus is pro-science and explores whether scientific knowledge and faith in God can co-exist.
Beside drawing several influences from Paradise Lost, The Atlantic 's Govindini Murty noted further influences, and wrote that "[t]he striking images Ridley Scott devises for Prometheus reference everything from Stanley Kubrick's 2001 to Leonardo da Vinci's Vitruvian Man and Mario Bava's Planet of the Vampires. Scott also expands on the original Alien universe by creating a distinctly English mythology informed by Milton's Paradise Lost and the symbolic drawings of William Blake."