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Beautifly first appeared in a picture as a Wurmple in A Trainer and Child Reunion!. Aaron explains that when he was younger, he loved going in the forest. One day he climbed up the tallest tree in the forest, but then, it was too tall to climb down. A wild Wurmple helped him climb down the tree and they then became best friends since then. However, Aaron lost his temper at it when they lost a battle, claiming that Wurmple was too weak, and he left Wurmple at the park. Aaron began to regret doing this and then went back to the park at night to see if Wurmple was still there, but it wasn't. Aaron regrets doing this.
In the same episode, when Aaron and the others' Pokémon were stolen by Team Rocket near the tree where they met, it came to their rescue in its fully evolved form by using SolarBeam. They were unsure where the attack came from until Beautifly appeared. After looking at it, Aaron realized that it was his Wurmple. It just wanted to be more powerful for Aaron, so Wurmple evolved into Silcoon, then Beautifly. It then remained with Aaron and the rest of his Pokémon.
Aaron does not possess a Beautifly in Pokémon Platinum, but this episode first aired after Platinum's Japanese release. This is similar to the case of Cynthia's Gastrodon, which also premiered after the release of Platinum despite being replaced with Togekiss. Beautifly was replaced by Scizor.