I think it might be based on the starting character you pick, as to how the plot unfolds. I didn't take the time to pick one of the other guy's besides Marty, so maybe it plays out different.
Also, I don't think it's so much you can choose who to work with, it's more like you can choose to use thier plan to complete a mission, in order to get bonuses, or you can choose to ignore/kill them if they become a pain in the ass.