The new Star Trek movie may not actually feature Khan Noonien Singh — or any other villain, for that matter. Co-writers Roberto Orci and Alex Kurtzman, who hope to have a script finished by Christmas, tease a very different storyline.
Orci and Kurtzman tell Collider they're debating between a couple of different ideas for the sequel:
The exploration sci-fi plot where the unknown and nature itself is somehow an adversary, or the villain model. That's an active discussion we're having right now. In terms of thinking about more than one movie, we want the movie to be self-contained in a way, but we're discussing the idea of having a couple of threads where if the second movie works, you could pick up into a cohesive whole. No thread more exciting and shocking for me when in "Star Trek III" you realize that Spock grabbed Bones and downloaded his Katra into him. When I saw "Star Trek II" I was like, "What's going on here?" and two years later, you're watching it and you're like "They're geniuses! They're geniuses!" So we're trying to think is there a version of that but again, "Star Trek II" does not rely on that thread, even though it turns out to be a thread. So we're thinking in those terms.
(Much more at the link.) [Collider]