Jirarudan is a pokémon collector and wants to collect all the pokémon, even the rarest ones. He had heard about how to get lugia, which is articuno, zapdos, and moltres' master, and the way is that he get all the legendary birds together in one place. So he goes out to find Moltres on its own island. Jirarudan uses ice to attack Moltres and captures it. Now Jirarudan is going on his way to Zapdos' island.
Meanwhile, Ash, Brock, and Misty are riding a boat out and let their pokémon out of their pokéballs to have fun. They start to relax as a storm hits them. They managed to quickly get on shore. They see that the people there are strangely dressed. Ash told them that he was a pokémon trainer and he was the only one on the island. They told him that they were having a pokémon festival and to goto get their power crystals at the legendary birds islands. Ash sets out on a boat in the big storm to moltres' island first. They quickly got off and sees that zapdos was there, looking for moltres. Then they spot Jirarudan holding moltres and he attacks zapdos, capturing him afterwards. He explains his plan to Ash and they start going to articuno island.
Prof Oak starts to talk to his friend about what was causing the storm. They start off to goto the islands and see whats wrong. Then in the moltres island, Ash is determined to free moltres and zapdos so Jirarudan wouldn't create an unbalance in the world to get lugia. They set moltres free with their own pokémon and moltres gets zapdos out. They both flew over to articuno island who was upset that he had created a storm and frozen the whole sea. They together start attacking Jirarudans airship and break it, causing it to fall on the shrine of the crystal ball on zapdos island. Ash retrieves the crystal ball and goes back to their ship with Misty and Brock. As Prof Oak comes in, he is being reported on news and says that the distruption of the legendary birds caused the whole world to be unbalanced.
Ash then brings the crytsal balls he got, which is 2, and puts them in their corresponding places in the shrine. As ash goes to find the 3rd crystal ball, the three legendary birds attack him. As one of them dive at Ash, a spout of water comes up and gets in the way, and at the top was lugia, god of the oceans. Lugia then begins to fight with the birds. As all 3 birds fight him at once, lugia falls into the ice ocean. The person from the festival which has followed them played a tune on her flute and revives lugia. Ash quickly starts going to articunos island to get the 3rd crystal ball to put the world back in balance. As he is on his boat on his way there, the 3 birds attack him, but lugia shields them all the way. Ash quickly climbs up the hill to the shrine where the crystal ball is. He grabs the crystal ball and runs back to the boat, but articuno makes a huge blast and blocks off the entrance. So lugia tells him to hop onto his back and so he did.
Lugia now has trouble dodging the attack of the birds. As he tries to fly back to the shrine that held the other two crystal balls, Jirarudan attacks lugia. Out of strength now, lugia falls down and falls into the ocean once again. Ash surfaces but is uncousious. Misty dives down to get him and he quickly comes back in a moment. He runs to the shrine and places the last crystal ball there. Then the girl plays the festival song on her flute again, and everyone watches as the water unfreezes, the grass and flowers grow, and eveything back to normal. The birds then return to their islands and lugia dives back down into his home, into the ocean. Ash and everyone waves goodbye as they all leave and is glad the world is again balanced.
