The movie starts with a man talking. He says: "My goal isn't to capture the god of ice, the god of fire, or the god of thunder. My goal is.... the god of water....". The computer informs him, "the god of fire is Moltres, the god of thunder, Zapdos and the god of ice, Articuno." It also tells him that they are located near the orange islands.

He tells the computer to go to the Orange islands, and scan the area for the closest Legendary bird. The computer finishes, and it tells him the closest one is the island of fire's bird. He tells the computer to go, and then there is a shot, showing the top of what looks like a huge building, which ends up appearing as a giant airship. It reaches its destination, and then starts to shoot shot of ice from a cannon.

The computer announces "Moltres has started to move", and then a giant stream of flame comes shooting out of the island, which Moltres comes out of.

The man says, "I've found you, god of fire." And taps a computer screen-containing desk, as a chess board. "Check.... mate." The airship shoots another ball of ice, which Moltres dodges, and then it deploys two rings, which surround Moltres, and start shocking it. After a bit, Moltres can't stand it anymore, and faints, and then the rings capture it in a small cage.

He announces: "My collection has grown by one. Next, is the god Zapdos, then on to Articuno. Then, to make my amazing collection complete, I will capture the god in the sea no one has ever laid eyes on, Lugia!"

Ash, Pikachu, Misty and Tracey are sitting on a boat, searching for the next island to get an orange league badge.

They decide that because the weather is so nice, they're going to let their pokemon out. They start letting their pokemon out, and they start to play.

Suddenly, a periscope comes out of the water, and it goes down to show a giant Magikarp, which Jessie and James are steering.

The sky starts to cloud, and the ocean starts to make large waves. Almost everyone on board almost falls off, and suddenly, a swarm of more than 50 Magikarp come from nowhere. Ash, Misty, and Tracey call back their pokemon back, while the captain of the boat tries to steer it, and Pikachu holds onto a pole.

Jessie and James' Magikarp ship starts to go off course, because of the Magikarp, they start getting control back, but then they suddenly start to swerve into a giant rock, which they hit and blow up.

The storm starts to calm, and they reach an island, which the ocean drift took them to.

The scene shifts to Pallet town, which is having a warm, sunny spring day. Professor Oak on a bike passes by, and comments on the nice weather, but then suddenly the sky starts to cloud, and snow. Ash's mom's Mr. Mime puts up an umbrella over her head.

Ash and Co. Get off of the boat, but are greeted by some strange looking people with bird masks with sharp sticks and spears. Ash and Co. start to nervously stare at them, but the boat captain calls out to one of them, and they end up being related. She takes off her mask, and says that there's going to be a festival soon. A girl, named Flura and not in costume comes out, and asks who Ash is. She turns her head away, not really interested in what he says.

Dumbfounded, Ash just stares there, but the boat driver answers for him. "A pokemon trainer". Everyone stares at Ash, including Flura. "A POKEMON TRAINER????" Flura comes down, and kisses Ash, which annoys Misty. Flura looks at Misty, and asks if Misty is Ash's sister. She angrily says no, and Flura then asks if Misty is his Girlfriend, and gets the same reply.

The town has a celebration, because it is the festival of the legendary birds. Ash and Misty are eating dinner, and Misty is still mad at Flura for asking if Misty is Ash's Girlfriend. Suddenly, a beautiful girl with a hand flute (sort of looks like an ocarina) starts playing her instrument. After Ash stares at her for a second, he realizes that it is Flura. She jumps down, and tells Ash that in order to calm the Gods anger, someone must find three treasures from three islands, and places them in a special place, while she plays her flute, they will be calmed. She also tells him that it is pretty easy to do. Ash immediately gets up, and decides to go.

The boat's captain says that she's ready. Ash asks if the others want to come, but all of them besides Ash decide to stay at the festival. Pikachu grabs Ash's hat, which was on the table, and suddenly runs towards the boat with it. Ash, Pikachu, and the captain get on the boat and leave.

Next, you see Jessie and James' destroyed Magikarp boat, with the top knocked off, with them paddling with their feet. They suddenly see a Pikachu, then Ash. Ash's big boat makes a huge wave, which suddenly knocks Jessie and James' Magikarp over. Shipwrecked, they watch Ash, wondering where he is going. It suddenly starts to rain and thunder, with the dark sky overhead.

"The god of Fire, the god of Thunder, and the god of ice's rage is increasing... Oh dear....". Suddenly, you can see a dark figure, which looks like a Yadoking.

The scene shifts back to the boat, going over big waves, and Ash, scared for his life, asking if this was supposed to be easy. The scene shifts again to Misty, Tracey, and Flura, with strong winds almost blowing the torches on the island out. Flura is worried that she sent Ash to his doom, saying that it was too easy. She decides to go after Ash. She runs out to the dock, and Jessie and James are there, crawling up from their wreck of a boat, and they see Flura, Misty, and Tracey. Misty decides to go too, and Flura asks why. She tells her that she's not his girlfriend, or his little sister, but she just wants to. Flura tells her that she just happened to want to follow him all the way here. Then, Misty gets INCREDIBLY mad at her, telling her that she just happens to go wherever Ash goes. Tracey catches up, and tells them that he does the same, and is going to travel with them.

They get on a boat, and they start on their way, hoping that Ash is still okay. Jessie and James have also stolen a ride on the ship, hoping to capture pokemon for the boss.

The scene next shifts to the giant Airship, with Geraldan in it. He realizes that because he has captured Moltres, the balance of the three birds was disrupted, and that the remaining two will try to control the land that Moltres had once had. The computer tells him that it appears that Zapdos is trying to take over, or move to Moltres' island. Suddenly, the whole world's strange weather patterns are from the deep, deep ocean currant, which effects the world's weather. At the same time, Ash's mom and Professor Oak are watching a weather report saying that in the middle of this whole deep ocean currents are right in the Orange Islands. Ash's mom starts to get worried, realizing that Ash is right there.

Professor Oak then gets a call from Professor Ivy, telling him that there are more different kinds of pokemon living in the Orange Islands, apparently for no reason.

The scene shifts back to Ash, and the boat driver. Ash notes that the sky is clearing up, because the rain is stopping. Unluckily for them, the ocean is still horrible, and they can't even steer the boat. They crash into the island, but the boat isn't that hurt, it's just on dry land. Ash gets off the boat, but the captain tells him to stay, because there is a risk of the weather starting again, but he tells her that he's going to grab the treasure, and come right back. He runs up the long rock staircase, leading up to the treasure. The scene goes over to Flura, Misty, and Tracey, riding a motor-powered boat on the rough waves, at top speed. Flura tells the others to hold on, and starts to go into the rougher parts of the water, then riding a wave. Suddenly, a big wave comes, and throws the boat upside down, but flips back over, before it hits the water again. Flura and the others hold on, but Jessie and James fly off of the boat.

The scene goes back to the boats captain, eating dinner. Out of nowhere, Flura's boat comes over the horizon, flies up, and lands on a rock, out of water. Ash's ship's captain comes out, and asks to herself what they're doing here. Flura asks if the captain is okay, but the captain tells them that the only one in danger is Ash. She tells them that Ash has gone out to find the treasures in this horrible weather, shocking everyone but her. Suddenly, Flura's boat starts to slip from the small rock platform they're on, but she suddenly pulls a lever, which brings up a sail. They start to float up into the air, using the sails to carry them up. Flura tells them that they're going up to where Ash is, and picking him up.

You suddenly see Geraldan, looking at Moltres, telling him that he cannot struggle out of the cage he has put him in. The computer tells him that Zapdos has taken over Moltres' island.

You then see Ash, running up the stairs. He tells Pikachu to stay back, but he keeps on following. He tells him again, but Pikachu keeps on coming. You can also Jessie and James hide behind a rock, waiting to capture Pikachu. Ash comes up to a shrine-looking place, and wonders what it is, but Pikachu comes up, and shows him that there is an orb in the shrine, which is the treasure. After a bit of struggling, Ash gets the orb out, and looks at it. The orb is strangely filled with fire. While he admires the orb, Jessie and James come behind him, and start the TR motto. He interrupts them, telling them that what he is doing is much more important than what they're up to. They pay no attention, and announce that they're going to capture Pikachu.

Suddenly, a giant flying boat comes down, and misses crushing them by inches. Misty starts to talk to Ash, but suddenly, Zapdos comes out behind them, and everything starts to crackle with electricity. Ash wonders what Zapdos is doing on Moltres' island, when Pikachu suddenly starts to shock Zapdos. Meowth tells TR that he's Pikachu isn't attacking Zapdos, but he is talking to him. They ask what he is saying, and Meowth says that Zapdos is telling Pikachu that if he was wondering why he is on the island, and not Moltres, it is because the islands master isn't there. As long as the master is gone, he will take over the island. Suddenly, he starts to shock something in the sky, which turns out to be the Airship. Everyone looks up to see it, and stares at its size.

And...... i can't tell you the rest otherwise it will spoil it for you......