When they show the counter at 0:05 there is no indication that it's under water. They state in the film that the blast radius is six miles. Hence, from bomb detonation point, you'd have to be three miles away. To fly three miles in one minute you'd have to be moving at 180MPH. When you add it all up, it seems like the Batplane is toast.
Yep. I made a point to pay close attention during my second viewing tonight.
He couldn't have dropped it in the bay, as JD just pointed out.
So that leaves two options:
Spoiler!
Either he bailed out at some point over the water, and let auto-pilot take over. Unlikely he'd survive considering it's winter-time, the rivers were iced over, the water in the bay would be freezing.
Or, he bailed just after struggling to gain enough altitude to clear that building (was the Bat Lucious took the EMP out of on top of this building?) with the explosion (Blake's "it's starting" comment on bridge") creating a diversion for the switch?
Again, maybe I'm off base here, but I really think there are three Bats.
1.) After the Wall Street scene, Bruce comes back to Wayne Manor in a Bat, and parks it in the cave.
2.) The next time we see a Bat, it's parked on the roof of a building - the Bat Fox takes the EMP out of.
3.) There is a gray, unpainted Bat in Applied Sciences in the beginning of the movie, and this appears to be the same Bat that techs are looking at with Fox at the end - they claim the auto-pilot software was patched 6 months ago.
All three could have been in play. We know at least two of them were.
The only other thing I can think of if he didn't physically switch Bats is that he flew out to sea, and the cockpit itself broke into a smaller vehicle, much like the BatPod did when the Tumbler was incapacitated. He then flew off, letting the auto-pilot take over for what was left of the Bat.
You'd have to think someone would notice this though, which makes me think he bailed earlier, potentially under the cover of that exploding building.