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The villains are from timelines where the main character either doesn’t exist at all, or isn’t a trainer to begin with. Pretty much all of them specifically state “If there was a trainer like you in my world things would be different”.
The idea is that (for the sake of the multiverse we’ll call this Rainbow Giovanni) Rainbow Giovanni went unchallenged in his mafia dealings since Red didn’t exist to stop him in his home universe, caught Mewtwo, and somehow gathered enough resources and knowledge to be able to willingly hop between dimensions whenever he pleases. The events of Goldenrod Radio Tower never happened to Rainbow Giovanni because he was never defeated.
Using this power he was able to hop to dimensions where other villanous leaders got their goals accomplished because their heroes weren’t there to stop them.
So Rainbow Maxie/Archie decimated their worlds but before they were about to die from the ocean/fissure Giovanni took them.
Cyrus commited genocide on a pretty much universal scale. Ghetsis rules Unova with an iron fist and most likely killed N for his dragon. Lysandre wiped out billions of people. All of them went totally unchallenged, and all of them would have insight for Giovanni to further gain power and multiversal domination.
The caviat is that whatever tech Giovanni had to dimension hop, Colress was able to duplicate to send these villains back to their own worlds permanently. Those worlds are still fucked.
