Satoshi and Alan continue their battle against Fleur-De-Lis. Satoshi and Alan's Pokemon are quickly being knocked out by his Mega Gyarados. Satoshi and Alan get help from former Flare-Dan member Pachira. Citron and Citroid are able to get into the Miare Gym to destroy Flare-Dan's control machine. Citron and Citroid are able to do so, but Citroid is destroyed in the process. Serena, Plantane, and Manon infiltrate Fleur-De-Lis Labs to rescue Harimaron. Hoenn Champion Daigo Tsuwabuki and Rocket Dan distract most of Flare-Dan's forces. Eureka is able to reach through to Puni-chan with her lullaby. Puni-chan and Z-2 are released from Flare-Dan's control.
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.