Main differences:
>It happens on LV-426
>Ship is named Magellan
>Weyland is after the terraforming technology, not immortality.
>Vickers is not related, but does have big aspirations in the company.
>There is a reference to Engineer Jesus, but Watts (who was religious in the movie) laughs it off.
>The main archaeologists (Holliday & Watts) are very intelligent and extremely excited when they find the dead bodies.
>There are several extra characters in the story, mainly scientists.
>Vickers also brings four soldiers as bodyguards and protection, all armed to the teeth.
>Fifield and the other dork are given a toast for being stupid enough to get lost in the pyramid.
>The Pyramids are terraforming devices, and they are made of living biological matter, capable of seeding worlds as long as they're fully terraformed.
>David does not poison Holliday at all, but Holliday does die by falling deeper into the pyramid and getting facehugged by an evolved facehugger. He gets back to the ship, is about to do Watts, and ends up going into convulsions and chestbursting. The xenomorph escapes and ends up killing a bunch of the crew.
>David is an evil d!ck nonetheless. He figures out the Engineer ship is a doomsday ship named Juggernaut and it was meant to deliver a lethal payload of xenomorphs to Earth, but they were attacked and killed by their own creatures. David has 2 protocols: the first was to discover the terraforming abilities, and the second was to eliminate the scientists. He grabs Watts, brings her to the "armoury" (where the ORIGINAL facehugger eggs are) and has her impregnated with an oldschool xenomorph.
>Watts does use the med bay, but it's to remove the new alien, not a squid baby. The alien escapes through a grate and Watts is left in the med pod for hours (not minutes like the movie), and she gets crazy extensive surgery. When she awakes she sees a soldier coming in and he is killed by the alien. While he's being fed on, she slowly gets out, grabs his gun, and unloads on the alien, killing it.
>The remaining crew (Vickers, Watts, a couple soldiers & randoms) go in to find David because he locked the engine controls to prevent escape from the moon. They find David, he resurrects an Engineer that was in stasis (last to survive massacre) and the Engineer goes apeshiat, rips David's head off, and attacks the others. Most escape, but Vickers and a soldier find resurrected Fifield (much grosser than the movie) and he attacks. He mortally wounds soldier, jumps on Vickers, but soldier shoots him and he erupts acid all over Vickers, essentially melting her to goo.
>The Engineer gets to the captain's chair (like in ALIEN where he's found) and starts to take off. Meanwhile Watts is driving back to the Magellan. Janek (ship's pilot) is in the command center when evolved weird alien attacks. It bites him, but Watts comes in and kills it with multiple head shots. They take off determined to ram the engineer's ship. During this the Engineer's chest erupts and a super alien comes out, thus leaving the Engineer where he was found in ALIEN. Ship starts descending, but David's head radios Watts and says auto-pilot is engaging. They ram the ship, Janek is killed, but Watts escapes in a pod. She has to do the same run-away as Vickers did in the movie from the engineer ship, but she does the smart thing and turns 90 degrees.
>Finally she has to fight the super xenomorph, kills it, and lives in Vicker's luxury pod while waiting for a rescue party and playing chess with Head of David.
>Each pyramid on the moon emits a beam/beacon into space . . .
THE END