On the way to Olivine City Ash and friends run into their old shutterbug friend Todd, who is now traveling far and wide in search of the dream photo opportunity - a close up of the Legendary Pokemon Articuno. Their reunion is cut short when a chunk of solid ice comes falling out of a perfectly blue sky. Out heroes examine the object and discover that a Sunkern is frozen inside. Observing the Pokemon to still be alive, Ash and friends rush it off to be treated at the Pokemon Center. They can't find one, and instead find a lodge run by a old lady named Sophia. She knows exactly how to treat the young pokemon. She then tells Ash and friends about the Sunflora that used to inhabit the mountain. They decide to head to the mountain to see if they can find some Sunflora, but wind up being attacked by Team Rocket. After Team Rocket is defeated, they continue their journey up the mountain. But will they find any Sunflora?

Ash, Misty, and Brock continue exploring the Johto region. They arrive at Mt. Quena, a special location in the Johto region famous for high winds and the Purity River, a river so pure that you can drink from it and feel immediately refreshed. A man named Cullen and his assistant Domino come to the nearby lodge to study the river. Team Rocket arrive and steal Pikachu. As they try to make their escape, the winds of the mountain toss them around and they wind up on top of the mountain. There, Domino reveals that she is actually a member of Team Rocket, and sends everyone on the balloon crashing into the lake on top of the mountain. After making it back to shore, Ash and friends once again encounter Mewtwo and his clones, and are soon caught up in the struggle between Mewtwo and Giovanni. Giovanni still wants to capture and use Mewtwo for his evil purposes, while Mewtwo wants to live a peaceful life with its clones and protect Mount Quena. Ash and friends vow to help Mewtwo in its quest, but will they be able to stop Giovanni, Domino, all of Team Rocket, and all their advance machines?