A long time ago, the people of Camaron Palace found themselves on the brink of destruction. Fortunately, they escaped it when Sir Aaron, the True Guardian of Aura, saved them. He sacrificed himself to stop a war between kingdoms. From that day on, a tournament is held every year to commemorate his noble deed.

Satoshi, a budding Pokémon trainer from Kanto, manages to win the latest tournament and is allowed to wield a staff said to have belonged to Sir Aaron himself. Lucario, the Aura Pokémon—who is also the servant of the True Guardian—emerges from the staff. However, remembering his last memory of his master abandoning him, Lucario runs away in confusion.

Meanwhile, Pikachu, Satoshi's companion, is abruptly taken by a Pokémon named Mew to the legendary Tree of Beginning. Only Lucario knows the way there, but he is unwilling to trust humans after his master's betrayal. Even so, to save his partner, Satoshi and his companions must acquire all the help they need and travel to the Tree of Beginning, unfolding hidden truths from centuries ago.