The story opens with the sight of Lizardon, Kamekusu, and Fushigibana defeated amongst Rocket trainers. High above them stands Myutsuu, atop a tower of rubble. Seeing that they will not win in this encounter, the Rocket agents turn and flee.

Waves crash up against the rocky shores of New Island. Myutsuu and his servant stand at the center of a domed room, screens staring down at them. One of these screens shows a cityscape, where two young men are engaged in a Pokemon battle...

Satoshi, and his Fushigidane face off against a rival trainer's Donphan. Upset at his defeat, the trainer unleashes three tough Pokemon and sends them after Satoshi...only to Have Pikachuu appear and win the day with a fantastic thunderbolt. Satoshi makes faces at the retreating trainer, and Kasumi grabs him by the collar, shouting at him for making them late. The three trainers, kasumi, Takeshi and Satoshi, take off running for the Pokemon Dome where a tournament is taking place.

As the tournament winner holds his trophy aloft, a bright light appears amidst dark clouds in the sky, and comes crashing down into the stadium. The crowd cries in surprise as the dust clear to reveal a mysterious stranger, cloaked with hood and scarf . The stranger releases three oddly marked Pokemon, who easily defeat the reigning champion's monsters, and send their pokeballs rolling to his feet. Without giving a name, The Stranger vanishes, leaving behind a mysterious challenge to the gathered trainers. Takeshi inspects the invitation, and finds it to include a map. Satoshi clenches his fist, fired up the idea of a fight.

Meanwhile, offshore, a kairyu flies out of the mist with the mysterious stranger on it's back. The stranger's hood has blown back, revealing Myutsuu's face.

Also off the mainland, Rocket Gang members Musashi and Kojirou spot the rare Kairyu and its rider returning to a small craggy island and decide to give chase in their comedic little submarine. However, their pokemon team-mate Nyasu has some reservations -- the island that the Kairu is headed for is property of the Rocket Gang, a research facility where the rare pokemon Myu was being studied...until the laboratory was destroyed. Musashi and Kojiro are unimpressed.

Meanwhile, on the island, Myutsuu is welcomed home by his servant and caretaker, a blank-eyed woman in dark and bulky clothing. She and Myutsuu converse briefly as she prepares the chamber in which Myutsuu sleeps. Night falls and Myutsuu dreams.

High above the Amazon basin, light clouds drift. A group of armoured Rocket grunts are lead by an elderly scientist, all carrying Master Balls. Their leader is Dr. Fuji, a man who has spent his life searching for Myu. Suddenly they are scattered as the glowing phantom itself zips through their midst, evading and destroying every pokeball lobbed at it. Dr. Fuji cries after it....and it stops. As Fuji gazes in wonder at the phantom pokemon, his team radio Sakaki, the leader of the Rocket Gang.

Dr. Fuji is obviously enamoured with the gentle creature, who lets him feed it, take hair samples, and even bring it inside his trailer, but realizes that the idyll cannot last. The Rocket Boss wants not simply Myu, but the most powerful pokemon in the world. There and then, wild eyed, Fuji begins his work. Myu watches in dismay, and quietly leaves the doctor to his tubes and liquids. Fuji is shattered when he realizes Myu has gone. In anger and madness he retreats completely into his project ...creating a replacement Myu.

With Myutsuu birth, however, Fuji's work is not complete. he becomes a sort of coach for the Pokemon, explaining the world and encouraging it in practice battles staged benefit of Sakaki. Myutsuu easily deflects a Nidoking's charge, impressing the Rocket Boss, but frightening his underlings.

In order to better control Myutsuu's dangerous strength, Sakaki has the Pokemon clad in insulating armour and put to the test again and again in battle. As Myutsuu fights, however, he thinks of Dr. Fuji, who seems so reluctant to see him used thusly. Sakaki, however, is very pleased with Myutsuu's abilities.

At night, Myutsuu stares at his reflection in the one-way glass inside his chamber as Sakaki stands outside. The Rocket Boss smiles a wicked smile as Myutsuu wonders what the purpose of all this training is.

Sakaki contacts Dr, Fuji, who is growing more and more displeased with the way in which his creation is being treated. Sakaki reveals his intent to have Myutsuu "mass produced", to create an army of undefeatable pokemon, with which to control the world. Fuji is horrified.

Initially unsure at what to do, Fuji at last makes a decision. He goes to the lab where Myutsuu is resting and helps the Pokemon to remove the insulating armour. Meanwhile, in the security room, all of the screens monitoring the lab and training facility turn to static.

Fuji grabs Myutsuu's shoulders and tells it of Sakaki's heartless intentions. Fuji tells Myutsuu that the guards are already on their way, and that the only way to stop Sakaki's plan, and to stop the future subjugation of Myutsuu's unborn siblings, is to destroy the lab...and the doctor...right away.

Myutsuu refuses. He tells Fuji that he could not do anything to harm his own father. Fuji is somewhat stunned.

The guards arrive and take Dr. Fuji away. As he is escorted down the hall, he glances over his shoulder at Myutsuu, with tears running down his face, and says what an honour it it him that Myutsuu considers him a father. Myutsuu's eyes narrow as the old doctor vanishes down the corridor.

The guards, armed and anxious, tell myutsuu to get back inside. Myutsuu doesnt respond. The image of the savagely grinning Sakaki passes through its mind. Myutsuu then fulfills Fuji's last wish, and destroys the facility in a fantastic display of psychic power.

It begins to rain as Myutsuu shifts the smoking rubble around him. tears mingle with rain on his face, and the downfall intensifies as he raises his hands and screams up into the cloudy heavens.

In the waking world, Myutsuu's servant looks on without remark as the Pokemon weeps in his sleep.

meanwhile, another storm rages. Trainers are caught at a small ferry terminal arguing with the harbourmaster about the cancellation of voyages. It's no problem for brave and headstrong trainers, though -- Satoshi ties his jack around his head and sets off on a doubtful Zenigame's back, and Kasumi wows a few onlookers with a quick swimsuit-change. Boijer, the harbour master, freaks out as trainers head out to sea (Takeshi in an inner tube). Both the trainers and the Rocket Gang are converging on one point....the island at the center of the storm.

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