Spoilers after the second paragraph.
Overall this is a brilliantly filmed, badly plotted story which is beautiful to look at, but fails to make you care about any of the characters, or really produce any noteworthy SF-nal musings. It's worth watching, but isn't a re-watch movie.
The story focuses on Elizabeth Shaw, whose father (a devout Christian) died of ebola (and whose mother, as usual, was off the scene even earlier). Shaw appears to be a variety of Raelian (someone who believes that humans were created or uplifted by aliens) and has discovered a series of images from many different cultures across many years showing humans worshipping a larger humanoid, and also what amounts to a star map. She believes this is an invitation to go visit humanity's creators, and convinces the head of Weyland Corp to fund a scientific expedition.
There's no indication as to why Shaw believes humanity was created by aliens, or why she thinks the creatures pictured being worshipped are aliens instead of gods. The same configuration of dots does suggest some link between the images (which were created thousands of years apart) but why not as visitors rather than creators? [Or as actual Prometheans, teaching humanity.] Tellingly, Shaw wears her father's cross, and when asked about the contradiction of beliefs, remarks that she might believe humans were created by what she called the Engineers, but that does not answer who created the Engineers. Shaw comes across as a very nice fanatic - hopeful, naive and obsessed.
The story's second protagonist, if it could be said to have one, is David. The question I expect most viewers will be wondering is whether David is a Bishop or an Ash - good robot or bad robot. We see him spying on Shaw's dreams while in cryostorage (making us all wonder why the hell she's _dreaming_ in _cryostorage_), (inexplicably) eating a meal he doesn't need, playing basketball on a bicycle, and watching Lawrence of Arabia - clearly modelling himself after Lawrence. Given Lawrence's story, this may either signal that he considers himself something of an alien among those around him, or that he has divided allegiences.
David fits into the creation story as the creation of the creation. If the Engineers made humans, humans have then made him. But he is an imperfect creation, without emotion, as Holloway (Shaw's boyfriend-colleague) insists on rubbing in at every opportunity. This particular David is referenced by a hologram of Weyland as his son. David dutifully wakes the humans up and is helpful and yet oddly passive aggressive - constantly making comments which drift through the edges of insult.
Once everyone is woken, we have several distinct groups. Shaw and Holloway, shiny-eyed idealists. The Crew (Idris Elba as Captain, and a few other people, just doing their job). Meredith Vickers, Company Woman, who seems to serve no purpose on the mission beyond being annoyed by it, and hating David. A Lot. Two token scientists - a geologist and what I think must have been a biologist. In the debriefing, it appears that many of these people have never met before, because there's nothing more logical than sending people to explore planets without telling them that beforehand.
They land. They find an underground installation. They set out to investigate. And here's where the plot and logic begins to fall apart. There's the usual idiocy of "this is a scientific mission, we don't need guns" which suggests that Shaw has no concept of, say, tigers in the jungle. David is clearly doing all sorts of stuff outside "look around, don't touch anything". The token scientists snark and quail, are surly and then stomp off as soon as things look worrying. Naturally, despite the computer generated mapping technology and the fact that their positions show up on it clearly, they get lost. They Get Lost. And nobody notices!
Scary chamber of goo is located. David secretly takes goo sample. Head of dead alien is brought back, and theoretically establishes that these very tall, white-skinned, black-eyed people have the near-same DNA as humans, thus somehow proving that they made us... 'kay...?
Unnecessary storm drama. Someone finally notices token scientists are stuck in the alien installation overnight, until the storm dies. What the two token scientists get up to, alone overnight and weaponless, is so unspeakably idiotic I can't even bring myself to detail it.
Why do they send such stupid people on trillion dollar scientific missions?
To untangle what's going on afterward, it's fairly clear at around this point that Weyland has brought himself along in cryostorage, hoping for a jolt of immortality from humanity's "creators", and is ordering David to investigate on his own, and do little experiments like give some black goo to Holloway to drink, to see what happens. [Which leads to yet another variation of alien baby, and Shaw having an emergency caesarian and then doing tons of dramatic running about afterwards. Shaw is superwoman.]
David finds one last Engineer still alive in stasis, and removes Weyland from cryostorage to take him down to wake the Engineer and ask for some immortality plz. Vickers, his daughter, thinks this is suicidal but she's obedient to his commands, as is David and the rest of the crew. The behaviour of everyone at this point is surreal - Shaw is running around all bloody after her self-inflicted caesarian and dead Mr Weyland is heading into the dig and everyone is just...disconnected, doing their own thing. I presume that everyone except Shaw and Holloway (and the two token scientists) knew the true purpose of the mission, but there's such an air of complete unreality about it all.
It's pretty damn obviously clear that the ship is totally full of jars of alien goo, and David later helpfully tells them it was heading to Earth, but only Shaw and the ship crew care about this. They figure that this world is some kind of bioweapon research facility and that the Engineers, after creating humans, decided to destroy them, and the goo is the bioweapon they planned to use, but it got out of hand and killed them.
Uninterested in this, all but Vickers and three core crew members head down to wake up the surviving Engineer and ask for some immortality plz. Weyland has David wake the Engineers and ask for immortality plz and the Engineer kills them all. Oops. Shaw sensibly runs away and warns the ship crew. Vickers is all for just leaving, but ship crew heroically sacrifices themselves to knock alien ship out of the sky, leaving Vickers to eject. Alien ship crashes, Vickers and Shaw run away, Vickers gets squished. [I think Vickers got squished because she was logical and selfish and driven and the character (other than the ship captain) I actually found by far the most interesting in the story. I wanted her to live.]
Shaw has obligatory final alien encounter, then retrieves David's head and sets off (in a handy other ship) to hunt down the Engineers' home world and again ask them why.
Yeah, total mess. I think we're supposed to come out of the film wondering about the creation of humanity, and what it means to create life in turn, and how Holloway was so dismissive of David, and David helpless to do anything but what Weyland ordered him to, while the Engineers in turn seem hellbent on destroying humanity for whatever reason.
So, you know Mary Shelley's Frankenstein? Subtitled "The Modern Prometheus"? We're meant to come out of this movie wondering if we're the Doctor or the Monster.
I came out of this movie thinking: "Why do they send such stupid people on trillion dollar scientific missions?"