Since there were legions of nine year olds who knew more about Star Trek than Harve Bennett did when he was hired to produce its new movie, he screened all the TV episodes, one after the other. The story that jumped out at him, he recalls, was "Space Seed," in which a genetically altered superman named Khan was found in suspended animation on a lost space ship from an earlier era (the very late twentieth century, still years ahead when the episode was made). He and his followers had escaped earth after they'd been deposed from ruling a quarter of the planet during the "genetic wars" they instigated. Khan, played by a young Ricardo Mantalban, is foiled in his attempt to take over the Enterprise, and Captain Kirk maroons him and his followers on a remote planet where their energies could be used to start a new life.

Bennett thought that revisiting the Khan character could make a terrific movie, and so that was the first thread. He drafted a story outline that had Captain Kirk confronting Khan, while rescuing a former love and her son, who turns out to also be his son. In the end, Kirk and son team up and warp off together.

Kirk's son and his former love would survive into the final screenplay, so that's the second thread.

The third thread was mothered by necessity. Leonard Nimoy was sounding very uninterested in appearing in the film, and the studio was worried that a Star Trek movie without Spock wouldn't sell. While the studio tried to figure out how much it was going to cost them to get him back, Bennett apparently decided to tempt him on a different level: he asked Nimoy if he'd like to play a death scene.

These days, Nimoy says he felt the Star Trek franchise was played out, and this would be the last movie. So why not go out with a death scene? But he may also have thought it was a better send-off for the character than simply walking away from it. Besides, death scenes are life to an actor.

Bennett told Nimoy that Spock's death would occur early in the movie, like the celebrated example of Janet Leigh in Psycho. Nimoy now says he thought that was a bad idea, but earlier accounts maintained that he was annoyed when various drafts of the screenplay kept pushing the death scene back towards the end.

In an alarmingly churlish interview for the DVD, William Shatner claims he came up with the basics of the actual death scene: Captain Kirk and Spock separated by a transparent wall (although he thought it might have been better if the wall wasn't quite transparent, and Spock would be seen just in outline. In other words, so Shatner would be the star of Nimoy's death scene. Sometimes it's very difficult to know where Shatner is kidding.)

The next thread came as a result of Harve Bennett's response to the first screenplay, by Jack Sowards, which featured a planet-destroying weapon. Bennett wanted a more positive phenomenon. Art director Michael Minor suggested the idea of terra-forming, which was a positive process of creating life, that would also have the consequence of destroying whatever already existed on the planet being terraformed. In the next draft of the script, this became the Genesis Project.

However, this script eliminated Khan. DeForest Kelley was unhappy with the scripts he saw, and he had to explain the Kirk-Spock-McCoy triangle to Bennett. He wasn't the only cast member unsatisfied. The story process was now officially in chaos, until writer-director Nicholas Meyer got a meeting with Bennett, read the scripts and when he met with the major cast members, agreed that they didn't have a movie yet. So he consulted with Bennett on which elements of each script and story so far they wanted to keep. They liked Khan's quest for revenge, Kirk discovering his son, the Genesis Project, and Spock's death.

And with that list Nick Meyer went off for a week or two and wrote a new script.

So now the story had Khan being accidentally discovered by a Starfleet crew, and extracting the information about the Genesis Project that would lead Kirk to him, and his vengeance. After Kirk discovers his son (a young scientist working on the Genesis Project) the Kirk-Khan duel takes its twists and turns. Khan is apparently defeated but manages to use the Genesis device as a weapon, and the Enterprise faces destruction, until Spock sacrifices himself to save the ship. But the Genesis device does create lush life on a barren planet, and (in a scene not in Meyer's script) Spock's burial in space becomes a soft landing on the new paradisiacal world.