As far as I know, they didn't. There seems to be a point where the events that occur here don't follow those of the game at all. Kanto I am familiar with, but I'd never heard of a region called Johto before coming here, much less the vast majority of Pokemon that exist.
...Then you have instances of Pokemon raining from the sky, which makes the least sense of most anything that I've experienced here so far.
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...Then you have instances of Pokemon raining from the sky, which makes the least sense of most anything that I've experienced here so far.