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The Primordial ship was originally meant to be the Alien Derelict/Juggernaut ship in Lindelof’s draft, but Ridley Scott thought it would be cooler to show something else.
The opening sequence was meant to be longer, showing a group of Engineers talking to each other in a proto-language.
In most of Spaihts’ drafts, the black material that consumed the Sacrifice Engineer transmuted, flew away and bit a primitive woman/man. Their pupils dilated and you could see something change inside them. Another version included a salamander-like hand reach out of the water.
There was a scene cut for financial reasons in which a submarine expedition are looking at a sunken city in the Mediterranean where they find a giant tablet with a star map on it. A different version of the script included an archaeological dig on Mars where they found ruins sharing similarities with ancient ruins on Earth.
In some of Spaihts drafts, Holloway and Shaw went to visit Weyland in his private residence, a space station orbiting around Earth. Another one included the couple travelling to Mars and visiting Weyland in his home which had a view of the terraforming work taking place on the planet.
Jon Spaihts imagined Holloway as an older person, perhaps inappropriately old for Shaw as a mate. Additionally Shaw was Holloway’s student at university.
There was a scene were Milburn discovers a little worm and talks about how important this discovery is. Lindelof mentions that this would have kinda explained why he was so excited about his later encounter with the Hammerpede.
Spaihts experimented with the idea that the Engineers saw in a whiter spectrum than human beings did. To David’s eyes, the ruins and catacombs showed interfaces that only he could see. Picking up clues that nobody else was picking up.
In the script, when David breaks the Ampule open, they cut to David’s POV and showed the black goo at a microscopic level.
In Spaihts version of the story, Holloway awakens a Facehugger while he is exploring the pyramid. He is implanted with an Alien, the “classic model”. The “Alien” burst out of Holloway during the love scene between Shaw and Holloway.
Spaihts’ draft included a cargo hold filled up with Alien eggs, David discovers this area. This scene revealed the purpose of the Juggernaut ship which was on its way to Earth to undo the human experiment. When Shaw follows David into the vaults of the ship, he deliberately infected her with a Facehugger. He also took her helmet so she couldn’t run back to the ship and save her life by using the med pod. She still makes it back there by holding her breath and using compressed air.
In the earlier draft by Jon Spaihts, a kind of classic chestburster is extracted from Shaw’s body during the med pod scene. The chestburster is then expelled from the pod and Shaw stays in there while it heals her. As she wakes up, she can see the monster grow up. Eight hours later the monster is full size and she’s watching it kill people through the glass.
Lindelof mentions that there was a two page dialogue exchange between David and the Engineer.
In Spaihts’ draft, the last Engineer died in the pilot’s chair. He had been infected and was carrying a Chestburster. It emerged from him while the Juggernaut was flying which caused the Juggernaut to falter on its path, allowing the Magellan ship to ram it. Shaw manages to eject from the ship just before the ramming took place. Then the Alien that just emerged from the Engineer comes out of the Juggernaut and the final action scene is Shaw being hunted by this creature.
Towards the end of the film, Lindeof talks about a deleted scene in which Shaw asks David what it is that the Engineer said to him during their earlier conversation. David tells Shaw that the Engineer told him that they did not come from there [LV-223] but a place called “Paradise”.
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