When Palutena notice a lot of Hades' minions were heading towards the Phoenix Mountain, she immedentily knew that they were after the Wish Seed. She sent Pit to stop the army and acquire the Wish Seed. However, in order to get the Wish Seed, Pit had to face the Phoenix that guards the Seed. Eventually Hades revealed that the Wish Seed was a fake, Pit still has to destroy the Phoenix to stop the war that continuously rages nearby. Eventually Pit manage to encounter the Phoenix and confronted it. Pit managed to destroy the Wish Seed, and defeated the Phoenix. Unfortunately, a beacon appears after the Phoenix was defeated which alerts the humans, making them think someone has taken the Wish Seed. This causes a large war to break out, just as Hades had planned.
Despite it getting defeated by Pit, the Phoenix returned in the Great Scared Treasure Trials. It fought roughly the same way as before. And just like before, the Phoenix was defeated by Pit.