Puni-chan battles against Z-2 to try and snap him out of Flare-Dan's control. Puni-chan is put under the same control as Z-2. Citron and the rest of the heroes battle against Flare-Dan's executives. Serena, Plantane, Manon, and a disguised Rocket-Dan go to rescue Harimaron from Fleur-De-Lis labs. Satoshi is able to free himself using his and Gekkouga's Bond Phenomenon and team up with a remorseful Alan to battle Flare-Dan's leader Fleur-De-Lis.
A young boy named Ash Ketchum embarks on a journey to become a "Pokemon Master" with his first Pokemon, Pikachu. Joining him on his travels are Brock, a girl-obsessed Rock Pokemon Trainer, and Misty, a tomboyish Water Pokemon Trainer who may have a crush on him. Ash and Co. end up traveling through various regions, including Kanto, the Orange Islands, and Johto, and then enter the Pokemon League competitions there.
Along the way, they run into many confrontations with Jessie, James, and Meowth, a trio of Pokemon thieves who are apart of an evil organization called "Team Rocket". But every time Team Rocket try to do their evil deeds, they fail thanks to Ash and his Pokemon.