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.

Damon”