THIS POST WILL CONTAIN SOME PROMETHEUS SPOILERS
I didn't find Prometheus to be much of a mystery overall but it definitely raises many questions. For example, I was left with many more questions about the origins of the Xenomorph (the Aliens from Alien trilogy) than I was when I went into the movie. However I'm pretty sure that Ridley Scott raised those questions on purpose(likely for a sequel), but the overall plot of the movie was fairly straight forward and there was not much in the way of twists or anything.
My main question, is what exactly is the Black Goo, and how did it lead to the chain of events in the movie. It seems that the Black Goo is some sort of aggression/evolutionary accelerant. Everything it touched was mutated into something bigger, stronger and more aggressive, and once that base creature had "evolved" into a monster version of itself, it would attempt to take a host and combine their DNA to create an entirely new and deadly creature. For example, that squid thing that came out of Shaw I would assume was an infected sperm from Holloway (from David putting the Black liquid in his drink) that grew inside her, and once it matured it attacked and impregnated the Engineer to create some sort of Xenomorph progenitor. A little bit like ta masculine version of the usual Egg>Facehugger>Human host>Alien evolution chain (Beginning at a sperm instead of egg... This might be way off I'm speculating here).
The Black Liquid seems to be a "weaponizing substance", it forces unnatural evolution and crosses DNA to make a bigger, more powerful weapon that spreads like a contagion, thus eliminating virtually any life it would come into contact with by making it essentially destroy itself. Even the birth of each new creature requires the death of the old host making it a hell of a genocidal weapon. It's almost parasitic if it wasn't for the killing of its host which parasites typically don't do.
There is also those Cave worm things that attacked the Geologist and the other guy. They were drowned in the Black liquid, and went from earthworm size to huge, pissed off and dangerous snake things(that interestingly had the acid blood quality of a Xenomorph). I'm not certain what happened to the guy that got the cave worm thing down his throat but it was badly injured and I assumed they both died before he was made host. The Geologist however got exposed to heavy amounts of the Black Goo and he began a rapid transformation into something that was once again insanely powerful and unrelenting much like a Xenomorph actually.
Which brings me to the last thing, the creature seen at the end. It looked a LOT like a Xenomorph but was created by a different chain of circumstances than a standard Xenomorph. I would assume the Xenomorph thing is the final stage of whatever that Black Goo was. After several stages of evolution a final host is found, and from there the infusion of the Black Goo combine with the DNA of Holloway (and his infected sperm), Shaw, and finally the Engineer leads to the creation of a Xenomorph. It would look different because the chain of evolution started with an infected Human, but I suspect the original Xenomorphs were spawned by something different before they came into contact with humans so it came out a bit different.
Am I looking into this too much?
Either way I loved the movie, and those Engineer's are badass. They are so fucking strong they almost nullify the threat of the Xenomorph aliens themselves.
There was also the question of whether the Engineers started all intelligent life, or if the one at the beginning that seeded the waterfall was just on earth. Also why did they leave a starmap for us to find them if they had intended to wipe out the planet. Early into the movie I was thinking they left us as descendants for a pure DNA sample to revive their own race should they die out, and the starmap would lead us to them to start the revival but that was quashed when I saw the violent intent.
So yeah having questions is very justified
. Even if the plot basics are simple the actual details raise many questions I'm hoping the sequel will get into.