Ash and friends are headed to Fallarbor Town when they are nearly hit by a Bagon jumping off a cliff. Ash sends out Taillow to attack the Bagon, but a girl named Michelle leaps out to accuse them of launching a sneak attack. After learning Bagon was at fault, Michelle apologizes and explains that her Bagon is trying to learn how to fly.
Ash challenges Michelle to a battle so Bagon can get more experience so it will evolve into Shelgon and then Salamence (which can fly). With Michelle using her special computerized glasses to guide Bagon, Pikachu takes a real beating from Bagon's Skull Bash attack.
The battle is interrupted by the arrival of Team Rocket in a helicopter. Meowth swoops down wearing a jetpack and grabs Bagon. Treecko hits the helicopter with Bullet Seed, causing Team Rocket to drop the remote control for the jetpack. Ash and the others run to find Bagon. Ash tells Michelle that she needs to encourage Bagon more so it can evolve.
Team Rocket meets up with Meowth and Bagon, discovering that Bagon is thrilled because it got to fly (using the jetpack). Ash and the others catch up, and Pikachu hits Team Rocket hard with Quick Attack. But Team Rocket captures Pikachu, flying off in their helicopter.
Bagon and Treecko use the jetpack to follow Team Rocket and attack the helicopter, freeing Pikachu. Pikachu zaps the helicopter, sending Team Rocket blasting off again. Bagon, Treecko, and Pikachu ride through the sky on the jetpack, and when they land, Bagon evolves into Shelgon!