What does that alien do in the prologue? Prometheus begins with one of those hairless, marbled beings nicknamed "The Engineers" standing by a waterfall on Earth, where he eats a mysterious substance and promptly dissolves. The opening credits take place over a spectacular landscape that looks like Earth, although Ridley Scott has hinted it might be another planet entirely. When the Engineer disintegrates, we see a close-up of a strand of DNA. Is this the source material for all animal life on Earth (I believe there are plants in the scene), or just genetic origins of the human race? My guess is the latter but what good does human genetic material do floating in a river?
How often did the Engineers visit Earth? Assuming the opening scene was on Earth (or at least something like it happened here), we know an Engineer visited at least once. But Noomi Rapace's character discovered matching cave paintings from ancient cultures that contained some kind of superior humanoid, as well as an astronomical map? Was this some kind of message encoded in the genetic material left by that first Engineer? Or were the ancient human societies visited by multiple Engineers (or the same one visiting multiple places)? Scott seems to think the latter.
Why does David spike Holloway's drink with that alien goo? The Vulture broaches this one, but doesn't articulate the theory that David wants to experiment with otherworldly materials as a key to human immortality. That's the reason, after all, that Guy Pearce was a secret passenger in the first place. Maybe David wanted to get a jump start on experimenting with human subjects.
What IS that alien goo? Presumably that nasty fluid is the bacterial form of the "xenomorphs" (the title creature from Alien, Aliens, etc.), which contaminates a living host and creates a blueprint for larval and adult xenomorphs compatible with the given species. If that's the case, though, it doesn't explain why the mutated Fifield attacks the Prometheus and its crew like a kill-crazy zombie.
Is Meredith Vickers an android? Idris Elba's captain straight up asks her if she's a zombie, and she counters by taking up his offer for sex. We don't know if they did it, and if that would have proven anything if they did. As played by Charlize Theron, she's a perfect physical specimen with interpersonal skills ranging from cold to homicidal. If she was an android, maybe she didn't realize it. (It's all very Blade Runner.) We'll never know unless they make Prometheus 2 with another model Charlize Theron on hand.
What happened to the Engineers on the planet? On "LV-223," human crew finds the corpses of the Engineers and dates them as 2,000 years old. Given that some had burst-out rib cages, apparently xenomorphs got loose and either infected or killed them all except the one in hibernation. For a minute the film seems about to reveal that the Engineer and ship we see will be the same ones discovered by the crew of the Nostromo in Alien, but it's not: the Engineer dies on the human's "life raft," not one of those horseshoe ships. Maybe another ship left LV-223 at the time of the same outbreak, the infected pilot died and crashed on the planet from Alien.
Why did the Engineers change their minds about humanity? We know that they cultivated the human race, but seemed prepared to use their biological weapons to wipe out humanity any doubts about their hostility would be dispelled when they woke the one from hibernation and he tried to kill them. Given that the Engineers have been around for many eons, it could be that their values have changed or they've split into vying factions. Or maybe they've judged humanity and found us lacking based on something that happened 2,000 years earlier. Which leads us too...
Why does Prometheus take place at Christmas? Idris Elba seems to be only one who cares that the mission takes place on December 25. He has a little fake Christmas tree and plays carols on the accordion. While the humans estimate the Engineers to have died 2,000 years earlier, which would've been around 193 A.D. on Earth, are the filmmakers trying to get us to think literally back to the life and death of Jesus? It's probably not a coincidence that Dr. Shaw, while sterile, was able to conceive thanks to Holloway's alien infection (although it wasn't exactly a virgin birth). And both the original, fire-bringing Prometheus and Jesus both saved mankind via personal sacrifice and we see that first engineer sacrifice himself. There's a lot of religious imagery going on for a film full of tentacle aliens with acid blood.