Maybe it's a case of Deja Vu, but this reminds me of something. I want to say the Pokemon Heroes movie (Latios and Latias), but I can't say for certain and no longer have the disk so I don't have easy access. Could also be another animated film that I'm mistaking it for. I might report back if I can find some time to rewatch it.

Not that movie. Still, I swear I've seen it before...