This is a great heartwarming story. I also like how you included yveltal, I have not seen very many stories that pull off a believable/friendly legendary. I was a little unclear on if the pawniard was a child of the scrafty (creative licenses could mean that the pokemon child does not have to be the same species as the mother haha), but that's just a minor nitpick. Keep writing!

[the rock Pokemon ]

You wouldn't capitalize animal or mouse or dragon, so you shouldn't capitalize words like pokemon or pikachu or charizard. The only time you should capitalize it is if you're using it as the pokemon's name, ie, Ash's pikachu is called Pikachu. This is because you only capitalize when it's a proper noun, which are the names of places or things. Similar reasoning should be applied to any other words you're thinking of capitalizing, like telephone or trainer. Or professor.

The bit with the boulder is unclear - why would a ninja frog mean knowing if a boulder was blocking a cave or not? It seems it'd make a lot more sense to push a rock to create a hollow and actually use it as part of what's blocking the rain. Or at the least to say the boulder was only partly blocking the cave, so the mouth of it was still visible.

Anyway, this was nicely done. I particularly like the idea of a stolen pokemon actually doing something about that on its own, and the friendship between the two was very sweet.