Just when it looks like Celebi is about to die, suddenly dozens of Celebi (possibly even the same one but from different points in time) appear and use their powers to revive their compatriot.
The ending is the best part. When Ash is still feeling low the Prof. tells him not to worry and does a Name Drop. Even then the kids DON'T PUT THE PIECES TOGETHER! The 4Kids people may think it's the audience that's dumb but in this case, Ash and the gang are clueless.
The part near the end of the film where the Marauder's Pokemon are free and now have a shot at recovery.