Giovanni wanted to controle the most powerful pokemon in the world so group of scientist including Blaine helped clone mew's DNA, it became so powerful that the scientists were not able to control it, most of the scientists died except for some few, and Mewtwo fled. Giovanni tried to show mewtwo that he's a friend, the pokemon believed him for a while until he realised it was a scam to make him a slave. So he blew up the hideout and hid inside a cave.