Mewtwo, who is newborn, opens his eyes in a laboratory, finding a dozen people in white clothes. They are scientists, who have given a birth to him, by genetically processing cells of Mew, the rarest monster on the earth, to create the strongest monster, able to speak a human language. Mewtwo's birth is not natural, but artificial. He recognizes that, and is confused, and destroys the laboratory. Giovanni, the boss of Team Rocket, takes him and makes him help them with capturing monsters. The mystery of his life is always in his mind, and he destroys the base of the gang, too, to be alone.
Overlooking the sea in a grassland on a cliff, Ash waits for Brock's stew, which is ready at a table. Misty helps Brock set up. Pikachu finds Togepi totter to the edge of the cliff, and panicked, rushes to help him. Togepi stops an inch from the edge, while Pikachu drops from it. The cliff is not deep at the side, to Pikachu's relief. Togepi chuckles to see him crawl up. A man challenges Ash. Ash cheers up, fights him to send Bulbasaur, Squirtle and Pikachu, and wins. Then a invitation card he receives, the message told by a beautiful woman in a hologram. The sender is unknown, who is just introduced by her the strongest Pokemon trainer, and is to have a Pokemon league in the Pokemon castle in New Island. Ash decides to accept the invitation.
A storm outrages waves of the sea, so that it is impossible to launch a ship, as his party arrives at a port. They learn that there are many other trainers who were invited by the stranger, and that a female doctor of a Pokemon center is missing. Trainers try the raged see, with the help of their monsters that can move in the water or fly. Anyone of Ash's party doesn't own those types of monster, and they don't know what to do. But a boat appears, and the two sailors offer a ride. Relieved, Ash accepts it. (He doesn't see Meowth at the head of the boat.) Ash is in high sprits in the boat, while Pikachu is scared of pitching. As a huge wave assaults it, the helmets which the sailors wore low over their eyes were swept away, revealing their faces. They are the couple of the Rocket gang, Jesse and James. Ash is astonished. At that time another wave comes, and they are all thrown out of the boat into water. Misty sends Starmie, while Ash send Squirtle. Ash and his friends hug each either, letting themselves totally in the stream. Then they finally reach the New Island they were invited to. So does the gang a moment later.
Only three trainers they find there were; Sweet, Sorao, and Umio. The woman who appeared in the invitation card tells them to send their monsters from balls, and they obey her. They are astonished when the host appears; he is Mewtwo, the monster who is unknown to them at the time. It is out of question that a monster is a trainer, which outrages trainers there. The woman's condition suddenly changes, and she collapses. Brock raises her in his arms, finding her a female doctor who they learned is missing.
Trainers send some of their monsters to fight Mewtwo, but he beats them easily. Then he takes the trainers and monsters to a league field he made.
The gang steals into the building in the castle, and happens to enter a laboratory. They find many huge tube there; some of them have a monster. As they wonder what is done there, Meowth is captured by a belt conveyer. He struggles to escape, while magic arms pulls his three hair out. Meowth manages to escape, seeing the computer beside the conveyer starts to work, and a copy of his is formed in a tube. Mewtwo, highly inteligent, studies there and successfully creats copies of Pokemon, that are stronger than the original. And they are not just copies; They have lives. Venusaur, Charizard, and Blastoise come out of tubes, then go to the league field, called by Mewtwo by telepathy.
Mewtwo knows that Sorao owns a Venusaur, Sweet a Blastoise, and Ash a Charizard. He is proving copies are superior to the originals. It is his revenge for human beings who have given a birth to him, making use of him. And copies are strong. They conquers originals easily, disappointing the invited trainers. Mewtwo's revenge doesn't finish. Weird balls he made flies across the field, each aiming at original monsters there. Mewtwo's balls capture them one after another, now leaving Pikachu. A dozen balls are sent to him. He runs, sometimes shooting an electric beam. Satoshi is irreated to be near him to help him. Finally, Pikachu is captured by a ball. Panicked, he runs after it which flies away.
In the laboratory the gang is, Mewtwo's balls which includes the trainers' monsters are carried on the belt conveyer. As magic hand takes one, the computer analyzes the gene, and creats the copy. Pikachu's ball arrives, and Ash follows. Those hands are stretching toward it--
Satoshi seizes it tight in both his hands, as the hands reach it, too. Ash pulls, with all his might, and some magic hands grabbed him, too. Ash gives another strong pull. Magic hands which on the ball and him are torn, sparking. The computer also breaks, and Mewtwo's balls spits monsters out. Pikachu is saved, too, and Ash hugs him tight in his arms.
Copies are summoned by Mewtwo and go to the league field. Ash and Pikachu follow them with originals. Then they see a small, white monster there. It was Mew. Mewtwo shakes his whole body with mixed feelings, dread and delight that he would fight his original to prove HE is superior. As they fight, monsters also battle with their copies hand-to-hand. The doctor says sadly, watching them fight, "They are copies, which have been created artificially, yet have lives, which are valuable equal to originals'." Pikachu's copy appears, too. He glares at original Pikachu, and beats him hard. Pikachu doesn't resist, is hit by the copy's blow, and thrown away--
Monsters, both originals and copies, fight, collapse, and fight... Only Pikachu doesn't fight, though harshly beated by his copy. The copy shouts at him, "pika, pikachu! (Fight me!)" Pikachu shakes his head, refusing to counter. Tears well up to the copy's eyes, but he cannot stop himself while Mew fights Mewtwo. Crying, the copy continues to beat Pikachu. Finally the copy is exhausted and collapses. Pikachu takes to hold him tenderly.
Ash cannot stand to see them battle any longer. He dashes toward the spot Mew and Mewtwo fight, crying, "Don't! Don't fight any longer!" Two monsters shoot sparks then, and they hit Ash. Screaming, he collapses to the ground. Monsters, including Mew and Mewtwo, freeze and just watch him.
"Pikapi!" Pikachu goes close to him, looking into his face. His body starts to stiff, and got rocky in a moment right before Pikachu's eyes. Pikachu wonders at first what is going on, sees his friend doesn't move, and shoot an electric beam at him, as he does instictively for fainted creatures. But Ash is still. Pikachu tries once more, then over and over. While he is too tired to shoot a beam anymore, Satoshi doesn't recover. Tears well up to Pikachu's eyes, roll down his cheeks, and drop to the ground, quickly filtered into the soil.
Other original and copy monsters begin to weep. Their tears wet the ground, and are conveyed to Ash through the soil. His body softens slowly, and he recovers finally. Pikachu hugs him, and Ash hugs back.
Mewtwo calls copy monsters by telepathy, and they floats up. He can now believe in his life, which is valuable, and is leaving to look for the place they can live. Ash, Pikachu, their party and other people and monsters see them flying away, now feeling for them.
When Ash is aware, he is at the port with his friends. Other trainers are there, too. Now one remembers what happened in the island. The storm is over a moment later, and the sea recovers the peace, its surface brightening in the sunlight.
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