Ash, May, Brock, and Max come upon the festival of the Wishing Star of Seven Nights. During their enjoyment, the legendary Pokemon--Jirachi, descends from the heavens and befriends Max. Jirachi, with the power to grant any wish, is sought after by many people wanting to claim its power. One man seeks to use its legendary power to revive an ancient Pokemon known as Groudon, unaware of the dangers hidden within Jirachi's powers

Deoxys, a Pokémon from outer space, terrorizes the high-tech city Ash Ketchum and his friends are visiting.

In the legendary past, before Poké Balls were invented, an aura-guiding hero Pokémon named Lucario sensed two groups of armies about to clash, and a threat of a massive war in front of Oldoran Castle in Kanto that would leave no survivors. He transferred this message to his master, the legendary hero Arlon, while he was being attacked by a violent group of Hellgar. During the battle, his sense of sight was lost and he was rendered unable to see. He used the detection of his Aura, and so with the offensive Wave Bomb, he eliminated them. Though by the threat, the queen of Rota, Lady Rin was resolute to die with her civilians, and so Arlon made a choice.

On their way through the Battle Frontier, Ash and friends meet up with a Pokémon Ranger who's mission is to deliever the egg of Manaphy to a temple on the ocean's floor. However, a greedy pirate wants the power of Manaphy to himself.