What happens to Giovanni in the manga/anime canon?
In the anime when Ash and friends reach the gym they find Gary beat them there. I believe they take off to go find Togepi whose gone missing while Gary battles Giovanni who uses the armored Mewtwo. Jessie and James eventually come across Togepi and present him to Giovanni who feels he's a useless Pokemon. He gets a call and heads out with Mewtwo leaving Jessie, James and Meowth in charge of the gym.