The movie starts off with Yadoking sitting on the beach looking up at the sky. The Yadoking see's Moltres, the legendary fire Pokémon. Yadoking is excited that he just caught a glympse of a Mystical Pokémon. Then Yadoking notices there is a large island floating up there. This is an artificial Floating Island that was created by Jiraldin, and he is up there to catch the Mystical Pokémon. He succeeds.

Zapdos is not far behind Moltres, and Zapdos flies down to the Floating Island to find Moltres captured. Zapdos gets mad and attacks Jiraldin. He is then captured.

After this display we find Ash and the gang on a Lapras, they end up on Yadoking's Island where Yadoking tells them what he saw. But first Yadoking warns the group that capturing any of the birds is a bad sign. Yadoking says:
"You must not touch the God of Fire, the God of Ice, or the God of Thunder. If you do the Heavens and Earth will rage and the world will head for destruction"
Pretty much he means if you catch one of the Mystical Pokémon the world will come to an end.

Meanwhile on the floating island articuno emerges from the clouds. Articuno flies around the Floating Island, Jiraldin attempts to capture Articuno but he fails. While Jiraldin is busy trying to capture Articuno the other 2 Mystical Birds manage to escape. Now that Moltres and Zapdos are free they fly up to join articuno in the sky.

Now the birds are circling the ocean, they begin to shoot out blasts of fire, lightning, and ice..all combining into one gigantic blast. The ocean rumbles and a huge cyclone appears. Yadoking is watching from the Island and he seems to know what is happening to the fait of the world, Yadoking is troubled and walks away. Back in the rumbling ocean the water starts to bubble, it suddenly calms and a huge mysterious Pokémon emerges from the sea. It is Lugia, God of Water!! Lugia joins the 3 birds to turn their wrath on all humanity.

In the distance a bunch of Pokémon that are gathering and watching . The rest of the movie is the 4 Mystical Birds running amuk wreaking havok...