Pokémon: Mewtwo Returns (2001)

Satoshi, Kasumi, and Takeshi continue exploring the Johto region, then have to rescue Pikachu after Musashi and Kojiro kidnap him. The search leads them to the hidden plateau where Mewtwo has established a haven for the cloned Pokémon from the previous film. The evil Sakaki is plotting to recapture Mewtwo and renew his efforts to create an army of bio-engineered Pokémon. Aided by the reluctant Nyarth, Ash and his friends defeat Sakaki and his henchman.