here is my theory:
At the end of the movie Lucius Fox and his mechanics were examining the Batchopper, which apparently cannot be the same chopper Batman used because that one was at the ground zero of a nuclear blast and was promptly vaporized, so obviously Fox had made more than 1 chopper; so during the final segment, Batman was actually flying a different chopper, he was remotely controlling the chopper that carried the bomb (firing missiles and maneuvers), since he fixed the auto pilot, obviously he can also hack & mod it in the process, so the chopper that got blew up along with the bomb was remotely controlled by Batman, and he was flying away in another chopper (presumably with Catwoman next to him) to the opposite direction at the same time.









