Flygon is a crafty Pokémon, being able to use its wings to create vibrations in the sandstorms it kicks up to create an alluring voice to draw people into its trap. It is also an experienced battler, being able to apply surrounding environment conditions and pick the appropriate moves.
As Flygon was sent out, it instantly devolved to Trapinch, and immediately turned into an egg. After the fight was resolved, the egg hatched back into Trapinch and rapidly evolved back into Flygon.
As Flygon was sent out, it instantly devolved to Vibrava, then Trapinch, and immediately turned into an egg. After the fight was resolved, the egg hatched back into Trapinch and rapidly evolved back into Flygon.
Goh first encountered Flygon in Mauville City while investigating a mysterious Sandstorm. When Goh encountered Flygon, he deduced that it was the one who had caused the storm. Goh immediately attempted to capture it, but Flygon easily repelled his Poké Ball. Goh and Ash then decided to battle and weaken it, with Goh leading out with Sobble. Flygon attempted to use Sandstorm, but Sobble managed to clear it with Water Gun, which also dealt damage to Flygon. After Flygon was hit with another Water Gun and three shots of Vacuum Wave from Ash's Riolu, it used Dragon Rush, which caused Goh to return Sobble to his Poké Ball to stop him from crying. Flygon then used Dragon Rush again, defeating Riolu. Goh then sent out Raboot. Flygon tried to use Dragon Rush again, but due to Raboot's heightened hearing, he could tell where Flygon was coming out from and dodge. Flygon attempted to decimate them with Draco Meteor, but Goh had Raboot jump from meteor to meteor, eventually shattering one, causing large rocks to crash down onto Flygon, sending him straight to the ground. Goh then used another Poké Ball, successfully capturing the Mystic Pokémon.
Goh enlisted the help of Flygon when he went up against the Legendary Pokémon Zapdos. It was revealed that Flygon had learned Dragon Claw and Dragon Breath during his time at Cerise Labs. Flygon managed to land a direct Dragon Breath on Zapdos, giving Goh a chance to capture it, but it managed to break out from its Poké Ball. After some encouragement from Ash, Goh came up with a strategy to defeat the Legendary. Goh had Flygon carry Raboot, bringing him up close to attack with Double Kick. When that also fails, Goh changes his strategy and has Flygon attack with Draco Meteor, which distracted Zapdos long enough for Raboot to get up close and land a Blaze Kick, which he learned just in time. Flygon watched as Goh attempted to catch Zapdos again, almost succeeding in doing so, before Zapdos managed to summon a lightning bolt, which destroyed his Poké Ball. When Zapdos was escaping, Flygon was too tired to chase after it, so Goh gave up on capturing it.
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Flygon was sent out alongside with Goh's Aerodactyl to help get Ash and his friends inside the alternate world and stop Dialga and Palkia from causing time-space distortions. They were both later sent out to battle the Alternate World Team Rocket. But Flygon rapidily devolved into Vibrava and then Trapinch before being turned into egg while Aerodactyl just devolved into an egg itself. Moments after the Alternate World Team Rocket was defeated, Ash, his friends, and their Alternate World counterparts, along with some help from Cynthia, Alternate World Professor Rowan, Jessie, James and Alternate World Nurse Joy prayed for Dialga and Palkia to stop fighting and pleaded them to turn their Pokémon back to their normal forms. Just then, a bright golden silhouette of Arceus appeared, calmed the temporal and spacial Pokémon down and destroyed the Red Chain that the Alternate World Team Rocket had them binded by. Dialga and Palkia then fixed the damage their fighting caused and returned everyone back to their respective dimensions, while also granting their wish to reverse the devolution effects on all of their Pokémon, returning Trapinch all the way back to Flygon and returning Aerodactyl back to normal.
At the Cerise Laboratory