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how can't you see it, the pokemon world and everything in it, both animate and inanimate are just different forms of Ditto. before time and space, there was Ditto. Ditto peered across the universe that was it and saw another universe adjacent, but this other universe was different; this other universe had space and time. Ditto saw this and became it. In this act Ditto became and birthed the pokemon universe as you know it. Ditto separated parts of himself and gave them consciousness, and thus created the species Ditto. These first Ditto were designated to replicate the stars, planets, and other masses. Later the Ditto would become the living things on those masses. Some Ditto, of course, chose to keep their original form and live like that, and some of those would later choose to appear to Trainers and travel with them (although these Trainers are just Ditto, a Trainer with a Ditto is actually just a pair of Ditto.) And it is in this state that the universe is still suspended, all just different forms of Ditto interacting with each other. There are no accidents, disasters, miracles, free-will, or flukes, there is only that ancient and powerful species the Ditto and every event that ever happens is only the will of one or more Ditto. Their ultimate intention is unknown to all but the Ditto, but since everything is Ditto everything knows their ultimate intention.
tl;dr everything is Ditto
now where did that first other universe come from? well that is a different story, and the existence of this current pokemon universe was the universe in question.
