Gotta Fuck 'Em All.
The villain took that as a challenge. One that he *completed.* Granted, he wasn't attracted to male Pokemon so he had to genderswap some all male-species (and discovered that several supposedly 'all-male' species like Hitmonchan had females, the Pokedex is LIES...), but he did, and one of every single breed of Pokemon, Legendaries and Mythicals included, all ended up riding his dick.
And now the Pokemon world, minus all the humans barring the female characters from the games (and a handful of guys he thought were hot) belonged to him and him alone.
Feeling nostalgic for those times, he appeared in a flare of power next to his private villa, on the beachfront. He looked around, feeling the ocean air wash over him, and sighed contentedly. He could sense his children by the Pokemon all around the world, remembering through his clones their births, and could sense the vast numbers of Pokemon he had impregnated (he counted his clones as himself since they shared a collective memory). All in all, he was content. Life was good on this world, he made sure of it. Everyone had a home, everyone had food and fun things to do...
And truthfully, there was a sense of gratitude that permeated everything's aura. He had come into the world finding it about to be destroyed in a few months time. Granted, he'd been selective about saving humans, but he'd brainwashed the survivors and the Pokemon of those he didn't save into believing he couldn't do much about that.
He is evil, after all. And he wanted all Pokemon for himself.
Arceus was upset with him for that, for being selective about saving human lives (even if she was grateful for saving all Pokemon by bringing their world to his universe), and the two had battled, ending with Arceus, the last Pokemon he hadn't fucked, being turned into a moaning, whorish slut like all of his lovers, begging for his babies.
Now Arceus was a happy cumslut Pokemon, carrying a new world growing in her womb, eager to feed and be fucked over and over and over again.
Yes, it was good to be Pokemon Master