However, God of Sea will appear then, quelling their angers--with an excellent trainer

A lithography tells a legend 'God of Flames, God of Thunder, and God of Freeze should not be interferred, or Heaven and Earth would be enraged, and the world would be destroyed. However, God of Sea will appear then, quelling their angers with an excellent trainer.' A collector named Giraldan believes the legend, and identifies that God of Flames is Moltres, the one of Thunder is Zapdos, and the one of Freeze is Articuno, each living in Earthia islands. He moves in a big ship Air Castle in the sky, and captures Moltres first. Aiming at the other two gods, he let the ship turn to look for them, noting the balance of the world begins to collapse--

Ash and his party travels Orange islands in a yacht, not knowing that Team Rocket follow them in a Magikarp-formed ship. Suddenly, the tide turns violent, jostling their yacht--and villains' ship. Their yacht is nearly engulfed by the whirlpools, but manages to reach a beach of Earthia's main island in which people hold an annual festival, led by a shrine maiden Flura, according to the legend mentioned above. Since they find that Ash is a Pokemon trainer, they ask him to play the role of the trainer of the legend and to go to the islands of Flames, Thunder, and Freeze for treasure, Poke-ball-sized transparent balls, which is said to quell rage of three gods. Ash and Pikachu are excited, and accept their proposal, starting in a yacht.

On the other side, Team Rocket also arrived at the island, finding Ash's party. They begin to follow him again... However, their obstruction is not so big trouble. He and Pikachu can see the sky turning dim, with dark clouds covering over it. Afraid of the whether, and getting over villains' attacks, they helps each other to gain two balls of Flames and Thunder.

In the main island, people worry about Ash, and Flura, Misty, and Kenji decide to start to help him. They can finally see each other, when Zapdos and Freeze duel in the sky for occupy the territory of Moltres which has disappeared. Giraldan's Air Castle appears then, and capture Zapdos, and by accident, Ash's party and Team Rocket and Flura. Kids and villains send their Pokemon, to destroy the mysterious cages which hold Moltres and Zapdos. As they can succeed, they escape the ship, following two rare Pokemon which left first.

Now the tree rare Pokemon fight near the island of Freeze. To quell their rage, they need three treasure ball, though Ash has only two of them. He needs to go and get the last one. He is scared, but Pikachu encourages him, telling him that he can help him always. Ash makes his mind up.

Ash and Pikachu make a sled from the broken yacht, and fleet in it on the frozen ground, pulled by other few Pokemon. However, when they are near their destination, struck by god Pokemon's attacks, their sled is crushed to pieces. Staring at the island of Freeze, Ash and Pikachu gnash their teeth, big disappointment in their minds. Team Rocket in a boat they made keeps up with them, and invites them to join them. It is the great help.

With Team Rocket's help, they can finally reach the island of Freeze, and have the last treasure ball, as god Pokemon's battle gets bitter and hard, blocking their way to destroy their boat.

In the deepest of the sea, something appears and goes upward, taking the ocean current. Splashing on the surface of water, it leaps out of the sea--it is Lugia, the God of Sea, Giraldan wants the best.

According to the legend, Lugia takes Ash who holds Pikachu on his back and flies, dodging their way through the battle field of three god Pokemon. When they are near their destination, Giraldan's cage assaults them suddenly, finally capturing Lugia. He flares up, and opens his mouth to spit a destructive beam, which hits to explode Giraldan's ship. Lugia then is totally exhausted, and drops into the sea, while Ash is also flown into the sea.

Flura decide to dive to save Ash, as Misty stops her. She says quietly, "he is a burden to me. So I'll go." She dives into the sea then, and successfully catch Ash and Pikachu in raging waves, and swims back to the shore, taking them. As he wakes and find himself, he is trying to the shrine in which he offered the first two treasure balls--to place the last one. Pikachu follows him, encouraging him.