Jirarudan approaches the Island of Fire in the Hikoukyu. He attacks it with ice, freezing the island and injuring Moltres. Weakened, Jirarudan is able to capture Moltres using an electric net.The flying fortress moves on toward the island of Thunder, and the weather begins to take a turn for the worst...

Ash, Kenji, and Misty are riding a boat (piloted by Mic-chan, a guide) to Ashia Island. They have just let their Pokemon out of their balls to relax when a storm blows in. Their ship is badly shaken, but Mic-chan manages to get it into the port (all but destroying it in the process).

Team Rocket are following Ash in their submarine, the Mecha-MagiKarp, and are hit by the same storm. They hit something and lose their rudder. Helpless, they are swept up in a school of REAL MagiKarp, which carry them towards the port but land them on the rocks instead...

Misty's mom is out on her front lawn when Professor Oak comes up on his bike, commenting on the nice weather. Out of nowhere, a herd of Digletts come down the road, picking up Oak's bike and carrying it with them down the road. Behind the Digletts come another huge group of Pokémon, heading in the same direction, South. Dumbfounded, the two notice that it has started to snow even though it is the middle of the summer...

Having landed at Ashia Island, Ash and his friends get off the damaged boat, only to be surrounded by a group of strangely dressed people. One takes off his mask and explains that there is a festival going on to celebrate the Pokémon Gods.

They are introduced to Furura, the Miko (a young girls who acts as the messenger for the gods) for the ceremony. She seems to like Ash, but gets on Misty's bad side (she first asks if Misty is Ash's sister, then his girlfriend.) The group leaves the beach for a pavilion where the ceremony will take place.

Mic-chan and Ash set out on the boat to the Island of Fire on the stormy sea and Team Rocket hitches a ride with them. Upon reaching the island, Ash runs from the boat up the stairs to the top of the mountain, where Moltres's shrine is located and where he will find the power crystal...

Misty and Furura decide to follow the others in a better boat. Team Rocket is climbing the stairs up the mountain when Furura's boat propelled up the mountain stairs by a wind sail jumps over them and into the depression on top of the mountain. Ash has gotten the stone and get ready to get into the boat for the trip back down when who should appear but Zapados! He is looking for Moltres and is very scared of something. He begins shooting out thunderbolts, his way of communicating. Pikachu begins to thunderbolt back, explaining why they are there and what they know. Their conversation is cut short when something from about begins to draw Thunder's electricity away...

Above them in the Sky hovers the Hikoukyu. Jirarudan attacks Zapados and he's captured like Moltres and imprisoned in the fortress. Now Ash and Furura know exactly what is causing the unbalance in nature. Ash and the others are now on a quest to rescue the birds from their captor.

Okay, somehow, they get on the fortress, and it would appear that Team Rocket helped them. Either way, once they're on the ship, they find the area where the Legendary birds are imprisoned. They're being held by the electric fields that they were captured in. They all notice that their Pokémon are acting strangely and Furura concludes that the unbalance between the legendary birds affects the behavior of the Pokémon. At about this time halfway across the world, Professor Oak is trying to explain the same thing to frightened people everywhere. Ash and his friends free the birds. But they birds are already outraged about their capture and not knowing who to trust, the birds attack Ash and his friends before leaving the fortress.

Once out of the flying fortress, Zapados and Moltres meet up with Freezer. The three of them fly together and create a gigantic whirlpool. The whirlpool emerges from the sea forming a water spout and at the top of the spout flies out Lugia.

Furura tells them about Lugia and that his presence means the destruction of the world. Satoshi runs towards Lugia and tries to warn him of the traps and plans that Jirarudan has already made for his capture. Lugia ignores the warnings but allows Ash to hop on before he begins his attack on the Hikoukyu. But Jirarudan was prepared for this and fires an electric cage, the same that had captured the birds, at Lugia. Lugia is knocked out by the attack and plummets into the sea. He recuperates, and continues his attack with the Birds until they finally destroy the Hikoukyu.