So, my spoiler-filled thoughts on Prometheus.
So many reviews have focused in on the seemingly illogical actions of the characters in Prometheus and how the plot doesn't make sense. I disagree. People are used to seeing the heroes of movies solve mysteries, overcome obstacles, and unlock puzzles, and Prometheus is an exercise in disregarding those assumed conventions. It is a movie about unsolved mysteries, unanswered questions, and wrongheaded ideas that lead to tragedy.
The movie opens on prehistoric earth. One of the Engineers, for reasons inscrutable, commits suicide by ingesting a substance that rips him apart at the genetic level, presumably so as not to contaminate Earth's infant biosphere. Here we have the first indication that the godlike Engineers, in fact, have feet of clay. They're incompetent. Again, audiences expect godlike technology to be flawless and magical, and it isn't, the genetic phage fails, and the tenacious Engineer DNA reasserts itself. Ultimately, its tenacity is sufficient to express its phenotype millions of years later, in human beings. (The sheer tenacity of Engineer genetic technology is arguably its defining characteristic, as seen throughout the film.)
Cut to our hero scientists, digging into a cave with paintings older than any yet discovered. Audiences are used to competent scientists, but what isn't immediately obvious is that these scientists are quacks. They're complete pseudoscientists, completely disregarding any archaeological preservation protocols and ignoring the fact that ancient cave paintings degrade rapidly when people expose them to fresh air and even their own corrosive breath. These are scientists who think "That's what I choose to believe" is valid reasoning, and disregarding three hundred years of Evolutionary theory has any possible basis in fact. It's pointed out to them, and their response is proof positive they're in total Cloud-Cuckoo-Land. They think the Engineers created us, but we in the audience already know they're wrong: humanity is an accident, a pernicious, self-bootstrapping form of directed evolution resulting from poor sterilization protocols. I suppose the Engineers felt guilty and meddled in some way once their blunder was discovered, leading to the supposed "star maps" across many cultures.
Peter Weyland, the tycoon who sponsors these cargo cult archaeologists, would hardly be the first wealthy benefactor to be taken in by wide-eyed frauds. He funds an expedition to go ask these Engineers who, the characters believe, are our makers, if they would perchance give him eternal life. Quite poetic and mythic, but these myths invariably end with the foolish mortals being destroyed. So it goes.
We arrive on the Engineers' world to find not a civilization, but what we eventually discover is a bioweapons facility, one apparently dedicated to wiping out all life on Earth. Perhaps as the result of some forgotten Titanomachia against the demigods walking among us, who knows? Not the audience, not the characters, though we are treated to much speculation which is probably wrong. The Black Goo created here induces mutations and violent behavior, as we see from the native worms growing huge and aggressive. Its basic effect on humans seems similar, even if its progression is interrupted early on by judicious use of a Weed Dragon. As the Engineers are, as we have already seen, less than perfect, their Black Goo escaped containment. Holographic recordings show a frantic flight to stasis pods, no doubt escaping some mutant monstrosity. The humans' arrival begins warming everything up and the pathogen begins seeping into the environment once again.
In the end, we find that not only were we not the Engineers' creations, not only is their technology tragically less than perfect, we find that they care nothing for us, and once put considerable effort into destroying us. They didn't, for reasons outside the scope of the characters' discovery, but the one Engineer found alive apparently missed the memo that the genocide had been called off. He has a payload of Black Goo that, we find, not only turns its immediate victims into violent weapons, also spawns all manner of other monsters. There are parasites on earth whose life cycles are no less convoluted, so I give this a pass.
In the end, Prometheus is a flawed film, but not for the reasons people think. It's a movie about hubris, about wrongheadedness, about unwarranted assumptions and believing too much in your own self-aggrandizing fantasies. Once you realize that the humans are wrong about literally everything they believe about the Engineers, that for once rank speculation doesn't turn out to be correct, you'll find you're watching a different movie than all the critics have been so unkind to. There are still plot holes, but so many things people think are holes are in fact plot points, and that much is being deliberately left unexplained, since the universe these characters inhabit is under no obligation to present them with any real answers, satisfying or otherwise.