Vignettelante 's right, there was a car switch thing at the end.
Also: Blow to the head. We are led to believe ("It's payoff time for Batman!") that Batman's about to catch some quarry at the Gotham Museum's Neanderthal exhibit, and the quarry's hiding with the... Neanderthals. Or is possibly TWO Neanderthals from the exhibit come to life. Very unclear. An adze or a rock (again, unclear) hits Batman on the head and he gets those little asterisk-y things around his head and looks confused, and then it's pages and pages of cracky Batman-eating-a-hotdog and Bruce Wayne fighting crime.
A villain called the Dodo Man is involved, and we see him at the end, when Alfred arranges for Bruce Wayne to go back to the scene of the injury or whatever and then Bruce finds a tracking device he put on a... um, Dodo (stuffed) and then 'instinct takes over' and it's all: "Quick change of clothes!" (at the museum, so he was carrying the Batsuit, apparently) and everything's back to normal.
I would have much preferred another blow to the head to fix things, because if there's anything Gilligan's Island taught me, it's that odd number of coconuts to the head = lose memory. Even number = Get memory back.