There was an alternate beginning to go with it. Basically, the beginning has Jason searching for Marie in that Greek seaside village. He gets sent in her direction, but collapses before he makes it (so apparently the movie is one big flashback). The ending has Jason waking from the flashback in a room with the white haired CIA guy (can't remember the character's name) inviting him to rejoin them "voluntarily" as "the world had changed." He then tells Bourne where he can find an unharmed Marie (they picked up her trail 3 months after she left France, and years had passed overall) and the movie ends with generic guitar-singer dude while Jason walks to Marie and they embrace.
They had this alternate beginning/ending idea after 9/11, thinking public opinion would now be for shady political assassinations and shadow ops. They did modify the original ending to the movie (apparently there were to be explosions), but at least they didn't go this other route.