Chaos erupts as Flare-Dan attacks Miare City with Z-2. Z-2 causes widespread destruction. With Alan's ties to Flare-Dan revealed, he is forced to take Satoshi captive. Alan instantly regrets what he has done after seeing what Flare-Dan's plans truly are. Meanwhile, Puni-chan transforms into the 50% Form to battle Z-2. This reveals Puni-chan's identity as Zygarde to the group.
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.