As Cruise himself describes, he, De Palma, and screenwriter Steve Zaillian came up with the general story of “Mission: Impossible” while Koepp was starting to write the screenplay. This was after the studio had thrown out a script by Willard Huyck and Gloria Katz (as detailed in the December 1995 issue of Entertainment Weekly). On the same commentary track, Towne reveals that the unique shooting schedule of the film allowed for small windows of time to open up, permitting rewrites to be done on the fly. While effects shots were being filmed, he and the film’s star would rework scenes to be filmed later in the week … or later in the day. Towne described the process thus:
“Fortunately for me at least, and then I guess ultimately for the film, what happened was that the first things that they shot was the blue screen stuff, on the train and everything else. And as that was going on, Tom and I, we would go over the scenes that were to be shot, and I would rewrite them in the middle of the night. And sometimes even between takes.”
Towne doesn’t reveal what the film was meant to look like prior to the re-writes, but clearly, he, or perhaps just Cruise, didn’t like what was happening. One issue that did arise, as reported by CinemaBlend, was a love triangle between Ethan Hunt, his boss Jim Phelps (Jon Voight), and Phelps’ wife Claire (Emmanuelle Béart). Evidently, George Lucas (!!!) saw the early love-triangle scene and asked personally that De Palma remove it. He did.
Like most Hollywood blockbusters, many, many people had a hand in the screenplay. What could have been chaos, weirdly hung together. At least well enough to warrant multiple successful sequels.