--Shamouti Prophecy
Lawrence III, a wealthy collector of the world's most valuable antiques, wishes to make his collection complete by catching the three legendary birds, Moltres, Zapdos and Articuno. Any one of them would be a priceless addition to Lawrence's collection, but he aims to capture the three in order to capture the fourth and most powerful bird, Lugia. Using his giant flying aircraft, Lawrence attacks the Fire Island, home to Moltres and captures the firebird. However, as Lawrence begins to follow the prophecy, the world's climate begins to be affected.
Somewhere in the Orange Islands, Ash, Misty and Tracey are traveling to their next island destination on board a boat owned by a woman named Maren. Team Rocket as usual follow in their submarine. Suddenly, both parties are struck by a sea storm and dragged across the ocean to the middle of the Orange Islands, where they arrive at Shamouti Island. The weather is also going wrong at Pallet Town, as witnessed by Professor Oak and Delia Ketchum. The trio and their Pokémon meet the islanders of Shamouti, who are celebrating their annual Legend Festival following the prophecy's tale - a Chosen One shall help Lugia to save the world and calm the legendary birds. Maren's friend, Carol was once the Festival Maiden, but now her younger rebellious sister Melody takes on the role with some reluctance, until she meets Ash and kisses him, angering Misty.
During the festival ceremony, Melody explains Ash's role as Chosen One. He must venture out to the islands of the legendary birds and collects three glass orbs that represent the elements of Fire, Ice and Lightning, bring them back to Shamouti's shrine where Melody will play a wonderful tune (similar to the cry of Lugia) which will end the festival. Ash heads out immediately, with Maren and Pikachu going with him. Pikachu seems to be the only one who realizes the seriousness of the weather and leads Ash to the location of the Fire Sphere on Fire Island, after Maren's boat crashes onto its shores. Team Rocket, Misty, Tracey and Melody show up later on, but the island is visited by Zapdos. Pikachu and Zapdos communicate using electrical attacks, Zapdos explaining he shall claim the island for his own. Lawrence's ship appears, capturing Zapdos and the rest in Melody's boat. Lawrence is very polite to his accidental captives and kindly releases them in the lower chamber of his ship where Moltres and Zapdos are held prisoner.
However, this proves to be a mistake when Ash uses his Pokémon to release the two birds, who immediately get into a fight and destroy the ship in the process. The ship crashes onto Lightning Island, where Ash finds the Lightning Sphere. The group escape onto Melody's boat while Moltres, Zapdos and new arrival Articuno duel overhead. A giant typhoon scoops up the boat and carries it to the Shamouti Shrine, where Ash and the others meet Slowking, the shrine's guardian. Able to speak, he shows Ash where to place the collected spheres.in the moment he places the Thunder and Fire Sphere, the legendary birds attack the shrine, but are stopped by the sudden appearance of Lugia. Lugia, who can also speak using psychic powers, explains that Ash, who is revealed to be the actual Chosen One of the prophecy, must collect the Ice Sphere from Articuno's island. Ash doubts he can do it, but support from his friends and Pokémon changes his mind.
As Ash sets out with Pikachu, Squirtle, Bulbasaur, Charizard, and Lugia towards Ice Island, Team Rocket witness a helicopter containing Professor Oak, Delia, Professor Ivy and a news crew crash land. Seeing a discarded inflatable raft and the helicopter's tail propeller, they get an idea. Ash's attempts to reach the island are thwarted by the legendary birds, but Team Rocket surprisingly come to the rescue on a motorboat using the items they salvaged. Team Rocket shock Ash by revealing that they do not wish the world to be destroyed. The heroes (and villains) race through the island and find the Ice Sphere. The legendary birds appear and Articuno is knocked out by its opponents. Ash, Pikachu and Team Rocket are saved by Lugia who heads back to Shamouti.
However, Lugia is slowed down by the extra weight of Team Rocket. The trio of villains decide to let go and nobly sacrifice themselves to allow Ash to save the world, something of which he is shocked by. Lawrence's ship, which is still functional, tries to capture Lugia, but it uses an Aeroblast attack to defeat the remaining legendary birds and Lawrence's ship before falling unconscious into the sea. Ash also falls unconscious but is saved by the timely arrival of Misty. Misty and Tracey revive Ash, who leads the group back to the shrine. Ash inserts the final sphere into shrine, which shines brightly with the unison of the spheres. Melody plays Lugia's tune, which revives him and restores balance to the legendary birds. Lugia takes Ash and Pikachu for a fly with Articuno, Zapdos and Moltres beside them. Suddenly, a giant stream of water rises out of the ocean (the Beast of the Sea) and is tamed by the song. All the birds return to their homes and the Beast of the Sea vanishes into the ocean.
Lugia also departs, thanking Ash for his help. After Lugia has left, Delia, Oak and Ivy arrive, Delia scolding Ash for his recklessness but then asks him if he could visit her once in a while on his journey. Ash agrees to her question. Lawrence picks up an Ancient Mew card from the wreckage of his ship, deciding to restart his collection on a smaller scale. The film ends with Team Rocket appearing on Shamouti, having survived their sacrificial fall, lamenting that nobody actually saw them being heroes - but Slowking reveals to them that many people watched them and are right now. Slowking looks towards the screen, breaking the fourth wall, as do Team Rocket, who end the film discussing what they should do now since they seem to now be good.
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