While Damon Lindelof is the one most credited with the final result that was "Prometheus", at one time the film was very much an "Alien" prequel with a script by Jon Spaihts that initially got Ridley Scott excited about the project.
Now, in an extensive interview with Empire, Spaihts reveals that the infamous 'facehuggers' from the "Alien" films were in his original draft and in particular were a key part of two scenes - the Shaw/Holloway sex scene and the much talked about makeshift surgery scene.
Spaihts says an unconscious Holloway gets facehugged in the chamber. Back on the ship and unaware, he has sex with Shaw and "it's while they're making love that he bursts and dies. So that lovemaking sequence echoed my original lovemaking sequence where he explodes! It was messy."
The other scene involves Michael Fassbender's David character being more malevolent: "Shaw goes to stop him and David ties her up and deliberately exposes her to a facehugger… David doesn't smell like a person - his breath isn't moist - so he can handle the thing like a kitten. It doesn't want him; it's not interested. But then he exposes it to her and it goes for her like a shot. He toys with her for a bit and then lets it take her. That, in my draft, was how Shaw was implanted with the parasite that she had to remove with the medpod sequence."
The full interview, with other juicy quotes, can be found here.