Update: Lindelof has responded to Slashfilm. We are including his response below the jump. He sheds some interesting light on the situation – but that doesn’t change the fact that Fox and Scott have no idea what to do now in regard to Prometheus 2.

Exclusive: Watching the 18 hours of extra features on the Prometheus Blu-ray I learned that Twentieth Century Fox didn’t trust screenwriter Jon Spaihts enough to run with his script, so they hired a big name to “clean up” Spaihts’ vision. This big draw was none other than “Lost,” Cowboys & Aliens and Star Trek Into Darkness writer Damon Lindelof, pictured.

Those of you who’ve obsessed over the quasi-Alien prequel as much as I have know that Spaihts’ vision was a one-shot**, meaning Prometheus lead right into Ridley Scott’s 1979 Alien. In fact, a source in pre-production at the time had leaked story details proclaiming that the movie takes place on the planet LV-426 where the elusive Space Jockey was first seen. At the finale of Prometheus, the Jockey ship that crashes is the exact same ship that Ripley and her crew discover in Alien. It’s a beautiful way to bridge the new sci-fi epic with the old one. But, if you saw Prometheus, you know that’s not what happened. The movie’s events don’t even take place on the same planet, occurring instead on LV 223 (which is ridiculous and means the Engineers are truly terrible at piloting their ships, crashing them all over the place).

Why? Greed took over.

Lindelof transformed Prometheus into a “trilogy”, thus stripping the first film’s conclusion of any meaning and setting Ridley and Fox up for disaster. This disaster was perpetuated when Lindelof announced he wouldn’t be penning the sequel. So, in short, the guy who convinced the filmmakers to make a trilogy, left them in the dust…

Sources close to the sequel have told Bloody Disgusting that the studio and Scott are literally “freaking out” over how to continue the story of Elizabeth Shaw (Noomi Rapace), and are taking pitches from basically anyone who can crack the story*. While a sequel is nearly inevitable, it definitely puts it in flux, and in a state of jeopardy.

*We expect everyone surrounding the project to deny this story. That’s standard procedure. Don’t believe ’em.

**Twitter follower @JonSheasby pointed us to a contradiction at Empire Magazine, where Spaihts says Scott and him talked trilogy prior to Lindelof’s hiring. You can read the bits below.

Spaihts tells Empire in an old interview: “I did have a plan for multiple films and the conversations I had with Ridley was about a new franchise, from the beginning. We talked about a possible trilogy, or a duology, but more often as a trilogy. And I did have pretty broad notions as to how we were going to get from this world to the original Alien – the baton pass, closing the circle, if you will. So yes, I did have plans for two other films. I came up with an even more twisted sequence than the Medpod, but I cannot tell you what happens…

“My vision of the trilogy would have involved the arrival of the Yutani Company and a couple of other major plays around the Engineers themselves: the revelation of an additional grand Engineer design, and the possibility of seeking an Engineer homeworld. That shot of the ship flying at the end offers a lot of creative ways to play with this. But it feels like it brackets you into the search for the Engineer homeworld and home civilisation. That’s an interesting challenge.”

In the end, the push to make this a new trilogy is causing a huge headache at Fox as they struggle to figure out the new film’s arcs. We’ll update you when we hear more.

2nd Update: Here is the response Lindelof gave to Slashfilm.

“While I’m happy to maintain my ongoing role as internets whipping boy (well, not happy, but at least resigned) this is a weird attack piece, even for someone who should be used to it by now.

The unglamorous truth is this:

During the creative process of Prometheus, all involved (that includes Fox and Ridley) had a strong desire for this film to launch off in its own way so that by the end, it would not connect directly to the original ALIEN, but instead run parallel to it. This is something that I talked about many, many times in the press burst around the release of the movie. As you probably remember, there was a lot of interest as to whether Prometheus was a “prequel” — the answer was, “Yes. Sort of. But if there was a sequel to Prometheus, it would not be ALIEN.”

Taking the strong foundation that Jon Spaihts had already written, I worked on the script to this end — and yes, during that process, Ridley did occasionally riff on what he felt might happen next as Shaw and David’s Head ventured off of LV-223 in search of wherever The Engineers had come from.

After the movie came out and discussions began about a possible sequel, I was already neck deep in writing and producing TOMORROWLAND with Brad Bird. I have found, unfortunately, that if I take on too many projects at one time, there is a higher probability of those projects sucking. And contrary to popular belief, I do not want anything I work on to suck. I really don’t. I care about these stories deeply — not just as a writer, but as a fan. It might not always feel that way to the audience, but I swear to God it is true. It also so happens that Ridley was about to embark on directing his next movie, THE COUNSELOR, and had another one, CHILD 44 lined up right behind it. The conclusion was obvious — In the best interest of the franchise, it was best to take myself out of the running before I had to suffer the embarrassment of potentially not even being offered it.

And that it is the complete (if not somewhat boring) truth.

As to whether Ridley and Fox are “freaking out” about me not working on a sequel, well that’s news to me. I retain awesome relationships with both. More importantly, the idea that there aren’t many, MANY writers out there capable of taking the reins is sort of ridiculous. I did not map out a trilogy and then walk when the going got tough. Anyone who says otherwise doesn’t know me and doesn’t know the truth.

The process of working on Prometheus with Ridley was one of the greatest things that has ever happened to me. Love or hate the result of that work, I don’t regret having done it for a second.

Bloody Disgusting was very clever in tagging their story with the sentiment that denials were going to come. This would seem to throw shade on me denying the veracity of the story simply by anticipating that I would.

But denying the story I am.

As I said, I will take all the abuse in the world for the things I have done, but I refuse to take it for the things I have not.

That’s my story and I’m sticking to it.

Your Pal,

Damon”