Soon after 9/11 — back when “everything changed,” before everything went back to normal — the filmmakers about to release The Bourne Identity were worried that their tale of a rogue black-ops CIA agent had the wrong tone. It was supposed to be *bad* that the CIA was running the secret Treadstone assassination program, but political debate around that time had swung quite forcefully in the other direction, with many people believing that the sort of thing that has gotten the CIA in so much trouble in the past was exactly what we needed in this “new era” of global terrorism.
And so the filmmakers shot an alternative ending, one that paints the movie as a flashback, a dream of an unconscious Jason Bourne, and when he awakes (post-9/11) he is offered his job back on a contract basis, with the explanation that “everything is different now” and that Treadstone was conceived by a “madman” who needed to be stopped, but “now is a time for madmen.” It is an interesting idea, and probably not a bad precaution on the filmmakers part, but by the time the movie was released in June 2002, things were already slowly merging back into normal, our long national nightmare was scabbing over, and the film was better off without the new sequence. It’s on the DVD as an extra, if you’re interested.