"Disturb not the harmony of Fire, Ice, or Lightning, Lest these Titans wreak destruction upon the world in which they clash. Though the water's Great Guardian shall arise to quell the fighting, Alone its song will fail. Thus the Earth shall turn to Ash. O, Chosen One, into thine hands bring together all three. Their treasures combined, tame the beast of the seas. From the trio of islands, ancient spheres shall you take, For between life and death, o the diff'rence you'll make. O, Chosen One, climb to the shrine to right what is wrong, And the world will be healed by the Guardian's song."
This is an intoduction to the three legendary birds Moltres, Zapdos, and Articuno, around which the plot revolves, introducing the theme of a delicate balance the forces of nature, embodied by the very Pokémon who represent them. Should the balance of power between these three birds be destroyed, chaos will ensue, prompting the "Great Guardian" Lugia to rise from the depths of the sea to attempt to end the senseless destruction, yet only with the help of a "Chosen One" destined to save the world.
A Pokémon Collector, Lawrense III, wishes to capture the three legendary birds and follow the legend's tale. This is all part of his plan to capture the Beast of the Sea, Lugia. Using a futuristic aircraft, he captures Moltres from Fire Island. As predicted, the world's climate and weather begin to go awry, alerting the attention of many Pokemon and humans, including Professor Oak. Along with Professor Ivy - who leaves Brock in charge of her Pokemin - and Delia Ketchum, he travels out to the Orange Islands in a helicopter.
Out in the Orange Islands, Ash Ketchum, Misty, and Tracey are on a boat piloted by Maren. Being on a very sunny day, they decide to let all their Pokémon out for some much needed fun. They soon find their old friends, Winnie the Pooh & the gang from the Hundred Acre Woods, who looks to join them on their little trip.
Soon, from Lapras to Psyduck, the whole gang are having fun. What they do not know is that Team Rocket is following them. However, a storm begins to form, striking both ships and Maren's boat is washed ashore onto Shamuti Island, the centerpiece of the Orange Islands while Team Rocket's crashes into a rock.
The weather is bad back in Pallet Town, too, and many Pidgey and a bunch of Diglett run towards the Orange Islands, along with Professor Oak and Delia Ketchum. Back on Shamuti Island, Ash, Misty, Tracey, and Pooh & the gang are welcomed by the festive islanders who are celebrating the legend. One woman, Carol, is old friends with Maren and was the former Festival Maiden. Now the role has been passed down to her younger sister, Melody, who takes a liking to Ash.
When Maren reveals that Ash is a Pokémon Trainer, the islanders declare him to be the Chosen One for the festival and is given the task of traveling to the islands of the birds and collecting three glass balls that represent the elements, before bringing them back to the island's shrine where Melody will play a song on a special instrument to end the task. Pikachu, who is rather edgy, heads out to Fire Island, Ash, Pooh, and Maren following.
They get caught in the seastorm again and crash on Fire Island. Ash, Pooh, and Pikachu locate the fire-based sphere; almost immediately, Team Rocket show up to cause trouble. Misty, Tracey, and Melody appear unexpectedly in Melody's aerodynamic boat, Melody feels responsible for sending Ash off. However, Zapdos suddenly appears and after communicating with Pikachu through lightning claiming the island as its own, it is captured by Lawrence III. Ash, his friends, and Team Rocket are accidently captured too. Inside, they free Moltres and Zapdos but the two birds end up fighting each other and cause the aircraft to crash-land on Lightning Island. Ash grabs the lightning-based sphere during the escape of the birds. The group escape in Melody's boat, and it is carried to Shamuti by a column of water, which is revealed to be Lugia. Slowking, guardian of the Shamuti shrine, instructs Ash to place the spheres into the shrine.
Ash is then instructed by Lugia to go to Ice Island to retrieve Articuno's sphere, and is surprisingly revealed to be the actual Chosen One as foretold in the legend, reluctantly accepting his destiny as he attempts the final task. Bulbasaur, Squirtle, and Charizard try to help Ash & friends get across the frozen ocean, but the legendary birds thwart their attempts. Team Rocket race in on a speedboat made from a dinghy and a motor salvaged from Professor Oak's crashed helicopter. Ash, Pikachu, Pooh, and Team Rocket race through Ice Island's undergrowth to the shrine where they collect the last sphere. The legendary birds fight again, and Articuno is knocked unconscious.
Ash, Pikachu, Pooh, and Team Rocket escape on Lugia but the extra weight is slowing Lugia down, so Team Rocket nobly sacrifice themselves to "save the world". Lawrence III then reappears and attempts to capture Lugia, but the legendary bird uses its signature move, Aeroblast, which obliterates his aircraft, as wells as knocking out Moltres and Zapdos in the process. But this weakens Lugia, who ends up tumbling into the ocean, defeated. Misty swims out into the ocean to save Ash, Pooh, and Pikachu, bringing them back to shore.
Ash, Pikachu, Pooh, Misty and Tracey head up to the shrine where Ash places the last sphere. Melody plays the song, reviving Lugia from the depths as well as the legendary birds. The weather clears up and Lugia offers Ash, Pooh, and Pikachu a ride in the sky. A giant underwater current rises from ocean like a sea dragon and follows Lugia around, tamed by the bird. The current goes back into the sea and the legendary birds deport to their islands, shortly following which Professor Oak and Ivy, along with Delia Ketchum, arrive and congratulate Ash and his friends. Lugia gives Pooh & friends a ride back to the Hundred Acre Woods as they give their good-byes, knowing that they will meet up again someday.
Lawrence III makes one last appearance, picking up his original Mew card, and walking away with a smile on his face.
Some time later, Team Rocket, having survived the fall into the ocean, make it back to Shamuti, whereupon Slowking says that they are not unsung heroes; he reveals that the audience knows they helped to save the world.
- Both The Tigger Movie and Pokémon: The Movie 2000 were released in 2000.