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Awright /vp/, fantheory time.
I'm sure someone else has thought of this before (hell, it probably has an official theory name like "coma theory" does), but it came to me the other day and sharing is caring, so here you go.
So Team Plasma, at least BW1 Team Plasma, was bent on separating the worlds of humans and pokemon, right? And it's been confirmed that the PMD world is separate from the other pokemon game worlds, and that there are no humans in it. Your partner in the newest game even suggests that humans only exist in fairy tales.
So, what if Team Plasma succeeded in liberating pokemon to such a degree that the world completely fractured, and the world of PMD is the pokemon world while the human world is the one we're living in right now?
Just a thought.
