Summary if you don't fancy reading the script.|
Spoilers, obviously for both PROMETHEUS and this screenplay:
There's no black goo. The initial transformation is done by a black cake that transforms into thousands of tiny black scarabs that bite the Engineer, consuming its DNA. Once the Engineer is completely consumed, the scarabs scatter and fly away. one lands on a primitive woman, and bites her. Her DNA begins to shift.
Shaw is named Watts. the Prometheus is named the Magellan. Holloway is actually a character. Their discovery is made underwater, looking at an Obelisk with Engineer glyphs. Research leads to them discovering the star map, as opposed to lining up a bunch of different pictures of five dots in a row.
They approach Weyland with their research to pitch him on paying for the expedition. Weyland never leaves Earth, and does not join their expedition. Vickers is not his daughter. He agrees to fund their expedition on the stipulation that if they find any technology there, Vickers takes over their operation and all technology belongs to him.
The expedition is to Zeta 2 Reticuli. The moon they land on is LV-426. The people who signed on signed on with no idea what they're exploring, but they signed on for Triple Pay.
David isn't altogether human looking - he's an early android model, and he has a very definite disdain for human-kind. He is programmed to follow orders until alien technology is found, and then he's programmed to get rid of Watts and Holloway as a means to protect the technological information Weyland is procuring.
Weyland doesn't want to know how to live forever. Weyland agrees to the expedition because he's been spending trillions trying to terraform Mars and it's not working right, and he believes he can reverse engineer the terraforming pyramids on LV-426. It is explained that the pyramids on Earth are likely human kinds attempt to replicate the Engineer pyramids. The "Jesus was an engineer" theory is brought up, but only as a throwaway joke and never mentioned again.
Fifield & Milburn aren't scared because they found a dead engineer, they're scared because the recording/apparitions are large, and loud, and screaming in a very deep voice. Fifield wants to bug out, Holloway tells him he's gonna have to walk if he wants to bug out because he's not lending them one of the vehicles they drove out there with. (said vehicle is what David uses to open the door, as opposed to pulling a ladder out of his ass as in the movie)
Fifield & Milburn get lost because they forgot to bring a map-reading module with them, and communications are cut off once the silica storm blows in. The Engineers aren't just dead - they've been murdered. some slashed - some chestburst.
Holloway is not sad that the engineers are dead, nor is Watts a practicing Christian. They're both happy that they've made the most significant scientific discovery of mankind's history, at which point Janek toasts Fifield & Milburn to becoming the first humans to freak out, get lost and sleep in their suits on alien ruins.
Milburn is still attacked by the Hammerpede, but it doesn't break his arm to get in the suit, it just bleeds on the suit and crawls in through the hole. Fifield runs away, and is attacked by scarabs, who eat through the visor on his suit and start biting him, transferring xenomorph DNA into his body. He begins to mutate.
David and Vickers initiate their takeover of the mission once technology is discovered. Holloway and Watts are led to the discovery at gunpoint by armed Weyland mercenaries. Watts accidentally falls down a shaft after another Recording/Apparition startles him. He falls into an egg chamber (there are no pedestals in this version, only eggs) and a soft, squidlike facehugger oozes onto his helmet, eats through it, and impregnates him. He comes to shortly afterwards and wanders into the map room/pilot room.
Watts/David find him, bring him back to the ship. Holloway tells Watts he can figure out how to get back to the Engineers home world, as this is just a way-station, not their home planet. He tells her to keep the pilot room secret from the Weyland people. In celebration of this new secret, they have sex. In the middle of sex, an alien bursts out of his chest. It tries to attack Watts. She locks herself in a closet. The chestburster flattens, and begins to ooze/squeeze through the cracks in the door. Weyland employees hear her screaming, the chestburster escapes through a vent.
They go back out to raid more technology, while Janek & his crew want to find Fifield & Milburn. Watts uses the data from Holloway's suit to find the map room/pilot room. David intercepts her, and leads her to a different egg chamber. This chamber is filled with regular xenomorph eggs. A face hugger emerges. David plays with it like a pet while explaining that these eggs were designed by the Engineers as a means to wipe out earth, but the engineers on LV-426 did their jobs too well and were murdered by their creation. He then lets the facehugger go, and it impregnates Watts.
Watts wakes up alone, and wanders back to the ship, sneaking into Vickers room and using her medpod. The medpod scene plays essentially the same, except midway through the cesarean, the chestbuster chews itself out anyway, and escapes through a hatch at the bottom of the medpod. The medpod locks itself down and repairs Vickers over the course of about 3 or 4 hours. She fades in and out of consciousness. The chestburster grows in size. A crewmember enters the room. It kills. It feeds. It grows exponentially, and molts/morphs, shedding skin and growing protrusions. She comes to just as the medpod is about to eject her, while the Alien is still in the room with her. She takes the dead man's gun and shoots the Alien in the head as it lunges for her.
The other chestburster has also grown, and is essentially boneless, pale, translucent xenomorph variant. It can morph between solid/less solid forms, absorbing bullets and folding itself into tiny spaces. It is white/translucent, with a visible skull underneath it's elongated head.
David leads them to the ship, wakes up the last Engineer. they have a discussion. Apparently by waking up the Engineer, the stasis it was in will speed up the incubation of the chestburster residing inside it, but before it pops, he'll set that course for Earth after all. It rips David's head off and starts killing people. Fifield ambushes the Weyland employee trying to escort Vickers to safety, rips him up. Jumps on Vickers. The employee lives just long enough to unload his clip into Fifield, who bleeds acid all over Vickers, killing her.
Pretty much everything from here out plays essentially the same regarding Janek ramming the Alien ship, the ship crashing to LV-426 and rolling after Watts, and settling, except the Magellan can only catch up to it because the chestburster pops through the Engineer piloting the ship before he can leave orbit, causing the ship to momentarily stall out before autopilot takes over.
When Watts wakes up after the ship settles, she still only has a few minutes to get to Vicker's lifeboat, but it's a giant xenomorph (called an Ultramorph) that is now chasing her, instead of the Engineer. She kills it after an extended chase/hide n seek sorta setpiece.
It ends with the other pyramids shooting giant beacons of light out of their tops towards outer space as Watts gets drunk and plays chess with David's head in Vicker's quarters, waiting for either Earth or the Engineers to send a ship after them