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?

Ash, Misty, and Brock are still journeying toward Olivine City when they come across a boy named Bucky who seems to be looking for something. He introduces himself and explains that he's looking for a Dunsparce. Recently, he and his family went away to visit his sick grandfather. When they came back, he found out that a swarm of Dunsparce came through town and all of his friends captured one, but now he doesn't have one. They decide to help the young trainer, but interference from Team Rocket could hamper that plan.