My friend and I just had a conversation about this the other day.

So, super intelligent pokemon, like Mewtwo, they want to destroy/enslave the human race or whatever….some punk kid rolls up with a pokeball, shoves him in it and suddenly Mewtwo doesn’t want to destroy humans anymore? He’d rather battle other snot nosed little brats and give up on his plans for world domination? What kind of sick brainwashing shit goes on inside these pokeballs?

I think if anyone were to try to capture him, he’d psychically shove a pokeball up your ass or better yet, he’d use his psychic powers to cram a person inside a pokeball and he would throw it at people. The latter theory assumes that Mewtwo is completely insane (think Deadpool).