Ash, Misty, and Brock finally arrive in Violet City, the location the first Johto Gym. They come across a Pokemon Academy. At the academy a young boy named Zackie becomes obsessed with Ash's Pikachu and decides to catch it, even if it belongs to another trainer. However, he ends up catching a Bellsprout instead. Meanwhile, the rest of the class goes on a field trip to the Sprout Tower, where Team Rocket is waiting for Ash so they can get Pikachu.

Fresh off his win at the Violet City Gym, Ash and friends encounter a Marill that cries at everything. Following an encounter with Team Rocket, Misty, Togepi, and Marill become separated from everyone after being washed away in a river. Now Misty must somehow get back to Ash and the others while at the same time passing all of the many challenges of a forest.