"Khan was in our mind," Orci said in the interview with John Champion and Ken Ray, set to be released Sept. 16. "When we were doing the '09 one ('Star Trek'), we can't help but fantasize about a sequel, like W.O.K. -- the Wrath of Kirk."
Orci said he and fellow writer Alex Kurtzman even considered adding the discovery of the Botany Bay, the ship Khan and his other superhumans were marooned on, to the end of the 2009 film.
But while Khan might have been a villain Orci definitely wanted to explore from the beginning, it didn't always stay that way.
"We started with Khan, went away from Khan, and then went back to him," Orci said.
There was a push early on to do Khan, and even create a rather "Heart of Darkess"-type story with the character, Orci said. The Enterprise crew would be sent someplace to catch Khan after a terrible act, and then be forced to work with him.
"We felt like we were falling into the trap of using a villain based on previous knowledge of the villain, and we were somehow relying on the audience's expectation to love or hate Khan to make that work," Orci said.
So the writers -- which included Kurtzman and Damon Lindelof -- tried an interesting approach: They created a villain that was not Khan, to see how that would work.
"What's the story?" Orci asked. "A villain that has his own situation that doesn't rely on anything."
They created a character that has been used by Starfleet, resorted to terrorism, is found by Kirk who is told about his abuse and how he's a victim of the "national security apparatus."
"There is a cancer within Starfleet, and it's a story you can pitch without saying anyone's name prior," Orci said. "Once we had that story, then it became, 'Now can it be Khan?'"
The choice to use Khan may have been obvious to Star Trek fans, but it wasn't so obvious to non-fans who turned out for the movie, Orci said. Plus, there was a desire to piece specific major elements of the Star Trek mythos together, and in this case, it was Kirk and Khan.
"You can't do Batman without The Joker," he said. "We knew it would be tricky, and we knew it would lead to a vocal outcry by some fans. But, you know, you have to make tough decisions, when you do something like this."