Heralded as director Ridley Scott's return to science-fiction, Prometheus combines the horrific monster violence of Alien with the pacing and sensibility of James Cameron's sequel, Aliens. Scott has always been quite open about the fact that he considered Alien more of a horror film than a true example of science fiction, calling it (in the film's DVD commentary) "fundamentally a thriller." That the his next film after Alien was Blade Runner, one of the most intelligent and most beloved science-fiction films of all time, both shades some viewers' memories of Alien and helped raise expectations that Prometheus would be a film about big ideas and not just one with big explosions.
For the first twenty minutes or so, Prometheus looks like it might meet those expectations. After archaeologists Elizabeth Shaw and Charlie Holloway discover cave drawings in various pre-historic locations suggesting that humanity's ancestors were aware of (and influenced by) visitors from another planet, dying tycoon Peter Weyland funds an expedition to visit the planet indicated in the drawings. Weyland hopes that its occupants can provide answers to cosmological questions such as how life on earth began and what will happen to him when he dies. Based on the drawings, they expect to find humanoid aliens, which they dub "the engineers" based on their belief that these life forms may have "built" life on earth. As anyone who has seen the first Alien film will suspect, what they find instead is an outpost decimated by some sort of attack. That it never appears to occur to anyone on the Prometheus that there could be a relationship between the deaths of the "engineers" and the mysterious pods oozing black oil they find in a room in the settlement is one of several places where plausibility is exchanged for brevity.
Gestures are made at a faith vs. science conflict—Elizabeth wears, loses, and regains a cross to symbolize her loss and rediscovery of religious faith—but despite some elevated language trying to equate meeting the "engineers" with meeting God and some exchanges about how humans and robots differ in relation to their respective creators, the premise of the film is never really developed beyond the point of providing a rationale for the ship to go to the planet indicated by the cave drawings. Once it arrives there, the film becomes a standard chase and escape thriller for the last hour; what had pretensions of being an origin story is revealed to be simply a prequel, more interested in settling questions from the first film—for example, what is the "Space Jockey" found by the crew of the Nostromo?—than in actually trying to think through or address the deeper spiritual questions the characters say they hope to have answered by making the quest.
Prometheus's biggest problem is not a lack of ambition, but of execution. The film is at no loss for ideas, but it can't really pause to catch its breath long enough to develop any of them. Ultimately, the film's themes fight each other for enough room to breathe, ending up as a pastiche of references to hot button issues rather an attempt to really leverage the alternate setting (as the best science fiction does) to tell us about our own world. There is a mini abortion-denial allegory, some (now standard) soulless-corporation skewering, warnings about the arrogance of science and the technological imperative ("anyone with half a brain and a swath of DNA can create life"), and even some anti-militarism. "Why do they hate us?" one character asks about those trying to kill the crew and, maybe, all of humanity. Whether this is meant to equate terrorists with soulless killing organisms or to suggest that terror wreaked on military-industrial societies is merely the blowback from their own, perverted drive to conquer and oppress others depends largely on whether you choose to believe the screenplay is subtly ironic or simply oblivious to many of its own implications.