My fan edit would be to replace the scene at the end of Supremacy, with him talking to Pam, with the opening scene of Bourne Ultimatum, where he escapes from Moscow. The final line of the film would be "My argument is not with you," and after he says it, "Extreme Ways" would start playing, it would cut to black and show a screen saying "To Be Concluded..." and then go to the credits. I think this would really be a great, powerful way to end the film. We've just seen Bourne finishing his emotional business with the Neski girl, and now he's out to finish what he started. It'd be cool.

The Bourne Ultimatum would then open with the scene where Bourne tells Marie's brother she's dead, to start the movie off on an emotional note. The film would then basically follow the exact same pattern as it did in the theatrical version, but, of course, the opening scene of him escaping from the cops in Moscow would never make an appearance. Opening with this scene, and with Bourne talking about finding the people who did this would open the movie emotionally, as well as with an "all business" theme, and would really start the movie off strongly.