Mewtwo realized the error of his ways, since it's voice actor was a guy in Mewtwo Strikes Back, and decided that what he was doing wasn't for the Pokemon or humans of the planet, and creating copies of them was against the freedom they deserved along with the love they deserve to be treated with. He took off with Mew and all of the copies to find them a place where they could live in place, but he doesn't have intentions of hurting either race anymore and only wants to live peacefully. He comes back in another movie in Japan soon but since i can't speak Japanese i can't say anything about it.