First it was announced that Ridley Scott's Prometheus was intended to be a prequel to his science fiction classic, Alien. Then Lost's Damon Lindelof was brought on to work on the script, and it was suddenly no longer a prequel but an original story. And then we heard reports that it may actually still be a film that takes place within the Alien universe. What the hay?

Lindelof has now shared his side of the events and whether or not Prometheus has ties to the Alien films.
It started as an Alien prequel. That is what everybody wanted it to be. Obviously, Ridley Scott has not made a science fiction movie in 25 years, since Blade Runner, so the idea that he’s returning to this genre is huge. But there is a real issue which is — what is the state of the Alien franchise at this point in our lives? There has been Alien vs. Predator and all these things, and its been completely and totally diluted. I’ve always felt that really good prequels should be original movies. And the sequels to those prequels should not be the movie which already exists because, with all due respect to anyone who makes a prequel, but why would you ruin the greatest twist in the history of cinema, “Luke, I am your father”, by showing me three movies which basically spoil that surprise. You can do movies which take place before Star Wars, but I don’t need to see the story of the Skywalker clan. Show me something else which I can’t guess the possible outcome of. There is no suspense in inevitability. So a true prequel should essentially proceed the events of the original film, but be about something entirely different, feature different characters , have an entirely different theme, although it takes place in that same world. That was my fundamental feeling about what this movie wanted to be.”

We shouldn't expect Predator to show up (until the second sequel at least). Lindelof also talks about how his contributions impacted the material.
“And truth be told, it wasn’t script doctoring in the strictest sense because the draft that existed before I came on was written by this guy named Jon Spaihts and it was very good. And there were a lot of things in the movie, Prometheus, which were Jon Spaihts and I feel like somewhere in the media reconstruction of this story, the tale is that I come in, I pitch an entirely new story, and its so original that everything else gets thrown out and that’s what we’re doing. In my brain, that’s not exactly what happened. But I also do feel that this movie is the movie I would want to see as a fanboy, take place in that Alien universe, which precedes the events of the original Alien, but is not necessarily burdened by all the tropes of that franchise with Facehuggers and Chestbursters, and all that stuff that I love…but its sorta like, we’ve seen it before, can we do something different this time? And thats the movie that Ridley wanted to make. And when you’re working with an auteur, you basically just shut your mouth and listen and try to transcribe and channel the vision of that person, and get out of the way.”

So it was Ridley Scott who pushed the story into more original territory. That's cool. I just still hope that something eats people in it. (via Collider)