Flygon made its debut to help Ash and Max rescue Jirachi from Butler to make him stop his plan to create a Groudon where it fought Butler's Salamence while Max and Pikachu rescue Jirachi. They did rescue Jirachi but couldn't stop the creation of Groudon, but after saving Jirachi Ash and Max said thank you to Flygon and it flew somewhere. After Groudon has taken Pokemon from the forest, the beast also captured May, Brock and Diane. After that luckily Groudon didn't manage to capture Ash and Max because Jirachi used its teleportation. The second try they almost got caught, but luckily Flygon managed to dive down and launched a Hyper Beam and freed Ash and Max. They tried to escape the blue vines from Groudon and Jirachi teleported again since they were almost caught. When Jirachi was absorbing the Millennium Comet. Flygon protected them with Butler's Salamence, but got captured by Groudon's vines. But at the end when Jirachi managed to defeat Groudon with a Doom Desire, everyone was freed including Flygon and it went away and not yet to be seen.
|Hyper Beam||Jirachi: Wish Maker|
|+ indicates this Pokémon used this move recently.*|
- indicates this Pokémon normally can't use this move.