I foresee it being a big screen retelling of the "Red Eyes" episode - which was the very first episode. Of course, that episode was the first episode and Faye, Ed, and Ein weren't on the show yet, so I assume the script will either already have them aboard the Bebop or will find a way to introduce them during the storyline. Of course, they may try to do away with one or more characters all together (Ed would be a difficult character to write for and cast, for instance). Plus, I'm sure they would explore Spike's past with the Syndicate, Julia, and Vicious - unless, of course, they were planning multiple movies.
So that's my take.