Christ I've written some shit. Okay it goes without saying that the music needs to be changed in scenes, lowered in volume in others. Then all the dialogue of the co-pilots are gone, the guy with the flamethrower can easily have his dialogue swapped for Fifield or David, all the 'inject DNA strand' and then show DNA thing can be easily simplified into just showing it. So that's all a given. I think I would write Prometheus as practically a direct sequel to Alien; I'd have it on LV-426 and have it wrap up the mystery of the Space Jockey there. So this is Prometheus, Wilbury style:
So it would start almost identically to Prometheus; a lone being by the waterfall looks up at a spaceship. But this time there's more emotion on its face; it's angry, upset, afraid. It opens the vial containing a white substance (that looks like android blood) and with some trepidation, drinks it. For a second he seems fine, before he collapses. He drops the vial and what's remaining seeps out; the white substance rapidly turning black. The being falls into the river (this time with some fishies in) and is ripped apart at the molecular level, lending his DNA to the Earth.
Then there's a title sequence, where each of the cave paintings is animated somewhat like the Skyrim teaser trailer with Alduin's Wall; so moving carvings and illustrations showing giant elephantine Cthulu type creatures lording over humans, holding some in their hands and pointing to the constellation in the sky. The sequence ends while resting on the one found on the Isle of Skye, with the scene between Shaw and Holloway.
Then it would go to David doing his thing on the ship but I would just cut out the scene with Shaw's father and have David standing there, obviously interested in something.
Then when they sit down in the little conference room, show the TED video, followed by the hologram of Weyland coming out. But old Weyland isn't played by shitty make up Guy Pearce, oh no... It's Peter O'Toole! Perfect casting and a little joke in regards to the film. He says his little thing about David and then tells them that his daughter Meredith will be overlooking things as she is taking over the company following his death.
Scanning the planet, Janek finds that there is two pyramid structures on its west side so lands in between the two. Shaw, Holloway and Ford go to one while Fifield, Milburn and David go to the other. I'd cut out the holograms here to keep some ambiguity and each of them come across an ampoule chamber. The giant human head is replaced with an elephant head but the ampoules are the same, save some greenish fungus stuff down the bottom (indicating the change into eggs). David grabs an ampoule, the other three grab the head and Fifield and Milburn start heading back to the ship.
Now the mural; I think you could leave it out entirely because the way it's depicted in the film is just fan service, but I'd probably change it so it's more of a hastily done carving like the star maps; the Cthulu creatures are bowing to a Xenomorph type creature, with some dead elephant figures around it. One of the Cthulus is pointing at a different star map to that found on Earth, so they note it down and go back to the ship.
How I'd explain Fifield and Milburn getting lost is they initially think they know their way back and by the time they do check the storm's interfered with their compass thing; Janek cant see a thing on any monitor so the squad just say they'll collect them tomorrow. Before the attack however, the two find some decomposed bodies with their ribcages burst; the large white creatures from the start and typical sized humans, both male and female on each side. They try and relay the images to the ship but obviously no one can see them, so they try and rest for the night. I'd probably swap Fifield and Milburn, so Fifield gets attacked by the worm and it goes inside him, while Milburn falls into the black goo. Doing this gets rid of the shit dialogue of Milburn trying to fuck the worm or whatever he's speaking to it for.
David poisons Holloway, Janek bangs Meredith, and then Holloway and Shaw just have sex. No conversation about fertility or babies, they just have rampant sex because they've been in stasis for so long and the build up of sperm must be colossal.
So the morning after they go into the pyramid structure which Fifield and Milburn entered, and they find Milburn's dead body face down in the black goo, with no sign of Fifield. They also come across the dead bodies. Shocked, they retain some flesh/bone/parts of both the smaller human bodies and the large humanoids and return to the ship. David has gone off by himself and found the pilot room with its stacks of ampoules and then instead of the pristine one in the film, there is a ton of bodies. Lots of them. 5 of the 15 foot elephantine creatures, and 20 to 30 smallish dead white Xenomorphs. David then is witness to the hologram of the planets.
Returning to the ship Holloway collapses and Meredith torches him. Shaw wakes up and this is when you find out she's infertile. David's there first but later Ford and another doctor, who she knocks out and then goes and caesareans the squid out of herself.
Then when she encounters Weyland O'Toole, David enquiries as to the whereabouts of the squid, and the awakened Ford goes looking for it but can't find it. Everyone gets told to be on the lookout for it, and then Weyland explains he wants to live longer and then explains why it had to be Charlie. He was the easiest to get the parasite into, Shaw's pregnancy was a ' happy' accident, they would use any means possible to try and find some sort of life form that would be able to help Weyland and infecting someone to see the effects was the easiest way. He doesn't say this but the reasons he's put everyone on the ship in danger a) because he's selfish and b) because he didn't even stop to think it would be dangerous. They've also done DNA tests on the body parts they've found and discovered that the large humanoids and the regular sized ones have identical DNA.
David mentions the pilot room in one pyramid so suggests going to the other one, which they do and find no bodies... but a Cthulu figure in stasis with a facehugger attached. David does all the steps he saw in the hologram and awakes the 15 foot being, and the facehugger just falls off him, dead.
Now here, you'd either have some sort of dialogue scene between the being and David/Shaw, either through vocal communication somehow or a telepathic scene where it actuallly shows what happens, or you could show what happens through a hologram, or you could save the answers for a sequel. But my thinking behind it is that the elephantine Cthulus are the Engineers, a race of incredibly clever beings that always strive to improve upon their own achievements. They first created life in small forms, that of the first amoebas to be able to live on Earth as it was the only hospitable environment they could find. They kept on creating and creating (and this could be some sort of theory that debunks Darwinism; did they create monkeys, dinosaurs, fish etc?) and eventually made what are the Engineers in the film but are in this just proto-humans; immensely strong beings at the peak of physical prowess but without the intelligence to back it up. This did not sate their thirst and so they modified the goo they used to create the proto-humans and eventually humans as we know them today were born.
Every few hundred/thousand/whatever years, they would visit civilisations and take some for further experimentation, giving them directions to constellations so that when humans were evolved and intelligent enough to have the means to visit, they would first be feted by the Engineers as a sign of their intelligence and power - and then matched up against their newest and most advanced creation; that of early parasitic creatures leading to xenomorphs. However the goo reacted and became self-aware. The Engineers tried to control it and test it by abducting humans and using proto-humans, forcing them to breed but ended up being destroyed and killed by the xenomorphs that had resulted from facehuggers, that had resulted from sexual intercourse with someone with a parasite inside them; the same method as Shaw. This Engineer was in control of the military testing ground and was attacked by a facehugger, being put into stasis and missing the whole battle between his kind and the rebelling xenomorphs. What he now wants to do is get rid of the bioweapon on Earth, wiping out humans and leading to a xenomorph breeding ground while the Engineers back on their home planet think of a solution to destroy the xenos; a) to regain their pride, b) to avenge their fellow Engineers, c) to save bringing it back home, d) to test what they already know, that the xenos would wipe out the humans and e) because it did not sate their thirst for science and they had to keep on creating new things. Like I say I don't know whether this would be through dialogue or some form, or condensed and kept for a sequel. That's just my thinking behind the whole xenomorphs already existing and their motives for destroying humanity.
So understandably he's pissed, rips off David's head because he's aware he's an android; he's really trying to save Weyland and Shaw from their creation because he was unable to save his kind. So he pops into his ship, Janek and the two co-pilots without dialogue because they're shit go smashing into the Engineer ship, making it DERELICT........
Weyland and Shaw have escaped by now but Weyland can't run very fast and is killed by falling debris (in a better way than Vickers was, it just comes from nowhere and squashes him), so Shaw runs for the escape pod, meeting up with Meredith and going to the escape pod. As soon as they walk in they see a dead Ford on the floor, and then Meredith is decapitated or something by the revived Fifield. The white worms have become parasitic entities like the things in fucking Resident Evil 4 or something, and have turned Fifield into something with the proto-humanoid being's strength and a human's intelligence, making him an actual viable threat rather than just a weird monkey man for two seconds. After throwing Shaw around for a bit the colossal squid kills him the way it does in the film, and Shaw knows that something is going to pop out his chest, so she flamethrowers the prone body just as the xeno starts to burst out of him, killing both the xeno and Fifield. The squid is obviously dead because it dies after impregnation.
David contacts her, and Shaw goes back to the ship, seeing the Engineer lying almost dead in his suit of armour in the chair. She sets a distress beacon to warn people away from the planet (!!!!!!) and then leaves to go to the other ship with loads of dead bodies but no alive ones, star map from the Xeno mural in tow which must be the Engineer's home planet, begging someone to go get help. And then a Queen Xenomorph bursts from the Engineer's chest, thus starting the cycle of Alien queen on LV-426 for Aliens, and all the eggs for Alien.
And that's my Prometheus film, written up while I was in work and inevitably as shit as the real one.