Ash finally arrives in Olivine City and is ready to battle the Gym Leader. At the Gym a girl named Janina arrives and claims to be the Gym Leader. Ash begins to have his battle with her, until the real Gym Leader, Jasmine appears. She apologizes for Janina, and says that at the moment she can not accept his battle because her Ampharos is sick. They head down to the Lighthouse where Ampharos is in order to help it. However, Team Rocket is planning on capturing the pokemon while it is weak.

Team Rocket's memories of Mewtwo had been erased, but the Team Rocket scientists' logs have not. After uncovering the logs, they track down Mewtwo and build a Base in a Johto. Ash and company meet Mr. Giovanni for the first time.