Jirarudan's a pokemon collector who wishes to capture the most rare pokemon of all, Lugia.  He hears of a legend that when the God of Flames (Fire), the God of Freeze (Freezer), and the God of Thunder (Thunder) are captured, then the Earth will lose its balance and the God of the Sea, Lugia, will appear to qualm their anger.  So Jirarudan's out to catch the three birds so that Lugia will appear.  Nevermind the fact that the Earth will be a mess afterwards...so Jirarudan heads for the Orange Islands, where the bird pokemon are supposed to be located.  First up is Fire.  Jirarudan goes to the Island of Fire and freezes the island with his giant flying fortress.  This drives out the weakened pokemon so that it can be captured with Jirarudan's electric rings.  The rings clench on to it and shock it, making the pokemon  unable to defend itself anymore.  Now Jirarudan has Fire, and is headed toward the Island of Thunder.  Meanwhile, the weather is starting to get bad as the Earth is becoming unbalanced...

Satoshi, Kasumi, and Kenji are on a guided ship ride to Arshia Island.  Satoshi-tachi let their pokemon out of their Monster Balls (as the Rivals remix plays) when the storm caused by Fire's disappearance hits the boat.  The guide, Michiko, is able to crash-land the ship to a nearby island port, but they destroy it in the process.  The Rocket-Dan, who have been following them the whole time in their Koiking sub, get caught in the same storm and crash into a rock, destroying the sub.  But they're OK.

Meanwhile, back in Masera Town, Ookido-Hakase comes riding to Hanako's house on a bicycle.  He comments on the nice weather before a herd of Digda carries Ookido's bicycle to the south.  Then another herd of pokemon starts to head south.  It starts to snow, and Ookido and Hanako comment about how strange it is for it to be snowing in the middle of the summer.  Ookido-Hakase calls Uchikido-Hakase (the scientist with whom Takeshi is staying with) and they agree to meet to discuss the possible reasons for the weather anomalies.  While Uchikido is talking, Takeshi makes his cameo, carrying a Nidoran back and forth. 

Satoshi-tachi have landed on Arshia Island.  The natives of the island are all dressed in animal skins (think Mononoke-Hime) and are having a celebration ceremony for the gods.  Furuura, a Miko (a communicator between the humans and the gods...Miaka from Fushigi Yuugi is a Miko) introduces herself.  Furuura leads the group to a place where the ceremony will take place.  Satoshi reveals that he is a pokemon trainer, so the island natives choose him to go to the three Legendary Islands (Fire, Thunder, and Freezer) to get three power orbs.  If Satoshi gets the three orbs together and puts them on a stone circle, and if Furuura plays her flute, the gods' anger will be calmed and the Earth will restore its balance.  Satoshi's boat is fixed and Satoshi and Michiko head toward the Island of Flames while Kasumi and Takeshi stay behind for the festival.  On the way, the Rocket-Dan, who have to peddle their sub manually to get it to move, see Satoshi and Pikachu come toward them on a boat.  The boat passes by and creates a huge wave, causing them to shipwreck.  Maybe next time, Rocket-Dan!  Maybe next time.

Back on the island, the storm gets worse, blowing out torch fires.  Furuura becomes worried for Satoshi and decides to go after him.  Kenji and Kasumi decide to go with her.  The Rocket-Dan land on the island and see the three kids.  They manage to sneak onto their ship right before they take off.

Satoshi's boat crash-lands on the island where the Fire Orb is because of the rough waves.  Michiko tells Satoshi not to go because of the bad weather, but he tells her that he'll just run in and run out.  Meanwhile, Furuura, Kasumi, and Kenji sail through the ocean at full-speed.  After having the ship tossed upside-down by a wave, everyone in the ship is OK except for the Rocket-Dan, who have been thrown off by the waves.  Ya na kanji!  Furuura-tachi arrive at the island, and Michiko tells them that he's not ready yet.

Satoshi climbs the stairs to the top of the shrine, wondering where the treasure is.  Pikachu points the red orb out to him, and after struggling a bit, Satoshi is able to pick it up.  The Rocket-Dan, who had been hiding behind a rock waiting to get Pikachu, stand up and say their motto.  Satoshi interrupts their motto and tells them that he doesn't have time for their shenanigans.  Suddenly, a large boat crashes in through the roof!  It's Furuura's ship--it had been carried by its sails upward by the winds of the storm outside. 

Suddenly, Thunder appears over Fire's island.  Thunder sends out electricity to communicate its distress, and Pikachu answers with its electric sparks.  The two pokemon talk for a bit while Nyasu translates.  Pikachu asks Thunder why it's on the Island of Fire, and Thunder replies that when the master of an island is gone, it is free to be taken over by whoever gets to it.  Suddenly, Thunder shoots its electricity into the air at an unknown object.  Soon, we can see what was shot at--Jirarudan's airship!  The electricity has no effect as Jirarudan's airship tosses rings out to Thunder which drains it of its electricity.  Thunder is captured, but Jirarudan also captures Satoshi, Furuura, Kenji, the Rocket-Dan, and the ship Satoshi and Furuura used to get to the island by accident.  Everyone's dropped off in a great hall, where Thunder and Fire are both in cages;  Thunder is struggling to free itself, but Fire has given up and just sits calmly.  Furuura notices a stone tablet telling of the legend of Lugia.  Meanwhile, Jirarudan's been informed of Satoshi-tachi's arrival and goes down to greet them.  He tells them of his plan and then returns to the bridge, for he is nearing the Island of Freezer.  He tells the kids to have fun and releases them. 

Ookido-Hakase is being filmed on his helicopter ride to Arshia Island.  He explains to the news reporters that the weather shifts are being caused by the unbalance caused by the capture of the birds.  Then Hanako tells the reporters that she's following Ookido-Hakase because her son is in the middle of the whole disruption and is in danger. 

Satoshi decides to free Fire first.  He sends out all his pokemon, and the combination of the various elements causes an explosion that frees Fire and Thunder.  Thunder attacks the ship from the inside, causing it to come crashing down on top of the shrine holding the Thunder Orb.  As Satoshi rolls from the crash, he notices a yellow orb rolling past him.  It's the Thunder Orb.  LUCKY!  Satoshi grabs it up as the pokemon overhead start losing control.

Meanwhile, all the pokemon start migrating south, sensing the Earth's struggle.  Those who cannot fly or swim travel to the southern-most shore that they can reach, waiting for a resolution.  Freezer, the pokemon Jirarudan hasn't caught, is losing control of its powers and as a result, the Earth's temperature drops significantly.  In fact, it freezes the entire sea! 

Riding a stream of water shooting upwards, Satoshi-tachi land near a Yadoking, who instructs Satoshi to place the orbs in the box that he has.  Yadoking, the evolution of Yadoran, is able to talk in human language and expresses its concerns over the fact that Satoshi only has two of the three orbs.  As Satoshi leaves to get the last orb, the three birds start attacking him.  Suddenly, just as Satoshi seems doomed, the mysterious water spout from before arises.  Soon Lugia, the God of the Sea, appears!

Lugia immediately begins to battle the three birds.  During the battle, Furuura notices that the sound made by Lugia is similar to the music that is said to be used to call on the gods.  The three birds join together and slams Lugia to the icy sea. 

Back in the helicopter, Uchikido-Hakase tells Hanako that the world is in danger because of the three pokemon.  Yadoking then appears and tells them that it's up to the chosen one to save the world.  The chosen one is Satoshi because he retrieved the first two orbs, but Satoshi explains that he only wants to be a Pokemon Master, not the person who saved the world.  This gets Furuura to thinking--if the legend of the three gods and Lugia is true, then her flute music should have some effect on Lugia.  Furuura plays the music she heard coming from Lugia, and the God of the Sea is revived.  Lugia flies over Furuura and tells her, telepathically, that the third orb must be put in place as soon as possible.  It also tells him that he must hurry to save the world.  Satoshi doesn't want to have the fate of the world on his shoulders, but his pokemon convince him to stand up and fight.  So he heads to the Island of Freezer.

Satoshi starts heading toward the island, on foot, but he soon realizes that the snow is too thick to continue.  Just then, he sees the wreckage of the boat he and Michiko used to get to the Island of Thunder, and the one Jirarudan captured.  Satoshi decides to make a makeshift sled out of the wreckage, and uses Pikachu, Lizardon, and Fushigidane to pull the sled.  Everyone else watches him as he does this.  Meanwhile, Ookido-Hakase and the others arrive on the scene, but are quickly knocked down by the fighting birds!  Their helicopter makes a crash-landing, and luckily no one is hurt.

Lugia does what it can to protect Satoshi as he rides the sled across the frozen sea, but a huge attack from Fire and Thunder causes the ice to break.  An iceberg lands in front of him and Satoshi is about to give up when the Rocket-Dan, in their own improvised vehicle (made using the propellers of Ookido's helicopter), do their motto and then invite Satoshi and his pokemon (now in their Monster Balls) to their vehicle.  They're helping Satoshi because if the world's destroyed, then there won't be anything left for them to steal.  As all of this occurs, thousands of pokemon watch the battle among the three bird pokemon. 

Satoshi arrives at the Shrine of Freezer, climbs the stairs, and grabs the orb.  Satoshi is ready to leave but Freezer, injured by the other two birds, crashes through the roof of the shrine and blocks the exit.  But Lugia comes in through the hole in the ceiling caused by Freezer and tells Satoshi to get on its back.  He does, and Lugia flies off (with the Rocket-Dan hanging by its leg).  Lugia dodges the birds' attacks for a while, but Lugia feels that it'll fail, so it tries to fly higher to lose the birds.  Lugia is ascending too slowly, and the Rocket-Dan feel that they are weighing him down.  So they let go, but forget that the ocean is frozen below.  They think they'll die, but the ice somehow turns back into water!  The pokemon surrounding them had made a hole in the ice to save the Rocket-Dan!  Yay!

Satoshi and Lugia near Arshia Island, where Satoshi needs to place the last orb, when Jirarudan reappears.  He fires a lot of electric nets at Lugia to capture it.  Lugia is able to dodge them for a little while, but soon it is captured.  Lugia shoots a huge beam of energy from its mouth and destroys Jirarudan's flying fortress and its net.  Then, still trapped in Jirarudan's rings, fires another blast at the three birds.  But this last attack has weakened Lugia, and it falls to the ground, breaking the ice and plummeting itself and the unconscious Satoshi into the sea.  Satoshi surfaces, unconscious, and Kasumi goes down to save him.  At first Satoshi isn't breathing, but he starts after a little time has passed, much to everyone's relief.  As this is happening, the three birds fall to the ground of a nearby island, unconscious.  Satoshi awakens, and immediately goes to the top of the shrine to place the last orb in place. 

The last stone is put in place, and a reaction between the three birds causes the stone circle to glow.  Furuura starts to play her flute music, causing the grass to grow again and the water to begin to flow.  The song is spread throughout the earth by the stone monoliths.  All the birds wake up, and the surrounding pokemon rejoice.  The waters calm down, the clouds clear up, and the sun shines again.  Lugia thanks Satoshi and makes the water the way it was before.  The three birds return to their respective islands.  The pokemon that had gathered to watch the battle all return to the wild.  Satoshi, who is still riding Lugia, lands and the two part ways.  Satoshi asks if he'll ever see Lugia again, and it said that it may, but he'll have to catch it himself.  The pokemon tells Satoshi to keep the legend of Lugia a legend, and Satoshi agrees.  Lugia leaves just as Hanako joins Satoshi.  She scolds him for getting himself in a dangerous situation, but is happy that he's OK. 

At the end, Jirarudan looks at the wreckage of the flying fortress.  He sees something shiny on the ground and picks it up...it's an Ancient Myuu card!

The Rocket-Dan are seen on Yadoking's island, feeling happy that everything's OK.

Then the end credits roll with Satoshi wandering around the Orange Islands as toi et moi plays in the background.

http://p2kmovie.warnerbros.com/