It's a sunny day on the road in Johto when Ash and his friends encounter a Yanma. Ash analyzes it with his Pokédex. Soon the Yanma flies over and steals Ash's hat. As Ash chases after it, Yanma's Trainer, a boy called Zachary Evans, orders it to stop. However Yanma ignores him and flies off into a nearby town. The local townspeople flee, seemingly afraid of Yanma's arrival. Soon Ash and his friends catch up.
When Yanma suddenly beats its wings, all the glass in a nearby bakery shatters. Zachary immediately recalls Yanma back to its Poké Ball, disappointed that his Pokémon has caused damage yet again. The baker carries Zachary off to see his dad, so Ash's group follow. Later, Mr. Evans, Zach's dad and glass-maker, makes Zach apologize to the baker, Mr. Strussel. Mr. Strussel says Zach should release Yanma, and Mr. Evans sadly agrees. Later, at a playground, Zach recounts how he first met Yanma to Ash and the group. According to him, there was a severe rainstorm a few months ago. Zach was helping his dad on the way back from delivering glass to another town when they spotted a Yanma lying on the ground. The two of them took it home and took care of it. However, as soon as it got better, Yanma broke all the glass in Mr. Evens' workshop. Zach decided to train Yanma but to no avail.
After telling the story, Zach decides to let Yanma go. Ash and the others are surprised, but Zach says that a window maker's son wasn't meant to be a Yanma Trainer. Soon, out in the forest, Zach says goodbye as he releases his friend before running away sadly. Zach later realizes he was wrong about releasing Yanma and returns to the location he released it in. When they head back though, however, Yanma is gone. Meanwhile, Team Rocket is out looking for the twerps when they see Yanma. Yanma lands by a river to get a drink and Team Rocket catches it in a net. Yanma tries to fly away, but it is tied down by a rope. Frustrated, Yanma produces a wave of air that breaks the windows in a nearby empty cabin.
Soon, Team Rocket uses Yanma to break glass in Zachary's hometown. Right after, Team Rocket, disguised as glass-makers, starts selling glass to the town and quickly turn a profit. Soon, Team Rocket rejoices with food, though don't give Yanma any. Meanwhile, Ash and the group are looking for Yanma without Zachary, and see a Pokémon Center. They hurry over and see Zach's dad inside. Meanwhile, Zach is out searching for Yanma in town and asks Mr. Strussel and two other people if they've seen Yanma. Mr. Strussel is frustrated by Zachary's attempt to fool him, and thinks he is connected to Team Rocket's window-breaking scam. Mr. Strussel picks up Zach and carries him off to Mr. Evans.
Meanwhile, Ash and his friends marvel at the stained glass windows Mr. Evans made, and he explains that he was afraid of Yanma breaking the stained glass too. Soon, Mr. Strussel appears with Zach and reports the young boy's window breaking antics to Mr. Evans. Then Meowth with Yanma on a string run past the Pokémon Center, while Jessie and James appear and recite their motto. Ash and Misty call on Chikorita and Poliwhirl respectively. Team Rocket then tries to use Yanma, but Mr. Evans stops them because Yanma would destroy the stained glass. Upon hearing this, Team Rocket says that Yanma will destroy the stained glass if Ash and the group try to attack. Jessie sends out Arbok, who wraps itself around Chikorita and Poliwhirl. Chikorita and Poliwhirl try to attack but don't want the windows to be destroyed, so they hold back.
Then, Misty tells Zach to try and return Yanma to its Poké Ball; Zach is successful. Chikorita uses Vine Whip and Poliwhirl uses Water Gun on Arbok. Though Victreebel injures the pair with a Razor Leaf. Then Zach has the idea to use Yanma in battle. Ash uses his Pokédex to check Yanma's moves. Next, Yanma uses Sonic Boom, knocking out Arbok. Victreebel tries a Razor Leaf, but Yanma dodges it with Double Team. Then Chikorita, Poliwhirl, and Yanma use Tackle, blasting off Team Rocket. The trio's profits are also returned to the townspeople. Afterwards, Mr. Strussel apologizes to Zach and Yanma for his earlier accusations. Later, Mr. Evans finishes installing the stained glass for the Center, while Zach and Yanma are now a team.