Mewtwo, a newborn, opens his eyes in a laboratory, finding a dozen people in lab coats. They are scientists, who have given birth to him, by genetically processing cells of Mew, the rarest Pokémon on earth, to create the strongest Pokémon, able to speak the human language. Mewtwo's birth is not natural, but artificial. He recognizes that, and is confused, then destroys the laboratory. The boss of Team Rocket takes him and makes him help them with capturing Pokémon. The mystery of his life is always in his mind, and he destroys the base of Team Rocket too, so he could be alone.

Overlooking the sea in a grassland on a cliff, Ash waits, Brock's stew is ready at a table. Misty helps Brock. Pikachu finds Togepi tottering towards the edge of the cliff, panicks, 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, and fights him with Bulbasaur, Squirtle and Pikachu, and he wins. Then Ash receives an invitation, the message told by a beautiful woman in holography. The sender is unknown, who is just introduced by her the strongest Pokémon trainer, and is to have a Pokémon league in the Pokémon 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 Pokémon center is missing. Trainers try the raged sea, with the help of their Pokémon that can move in the water or fly. Nobody in Ash's party own those types of Pokémon, 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 note Meowth at the head of the boat.) Ash is in high sprits in the boat, while Pikachu is scared of sailing. As a huge wave assaults it, the helmets which the sailors wore low over their eyes were swept away, revealing their faces. They are 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 and Ash, Squirtle. Ash and his friends hug either of them, letting themselves totally in the stream. Then they finally reach the New Island they were invited to. So does Team Rocket a moment later.

Only three trainers were there; Sweet, Sorao, and Umio. The woman who appeared in the invitation card tells them to send their Pokémon from their pokéballs, and they obey her. They are astonished when the host appears... he is Mewtwo, the Pokémon who is unknown to them yet. It is out of question that a Pokémon is a trainer, which outrages trainers there. The woman's condition suddenly changes, and she collapses. Ash raises her in his arms, finding her a female doctor who they learned is missing.

Trainers send some of their Pokémon to fight Mewtwo, but he beats them easily. Then he takes the trainers
and monsters to a field he made.

Team Rocket steals into the building in the castle, and happens to enter a laboratory. They find many huge tubes there; some of them have a Pokémon. As they wonder what is done there, Meowth is captured by a belt conveyer. He struggles to escape, while magic arms pulls his three hairs out. Meowth manages to escape, seeing that the computer beside the conveyer starts to work, and a copy of him is formed in a tube. Mewtwo, highly intelligent, studies there and successfully creats copies of Pokémon, 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 field, called by Mewtwo using telepathy.

Mewtwo knows that Sorao owns Venusaur, Sweet a Blastoise, and Ash a Charizard. He is proving copies are superior to the originals. It is his revenge for humans who have given a birth to him, making use of him. And copies are strong. They conquer originals easily, disappointing the invited trainers. Mewtwo's revenge doesn't finish. Weird Pokéballs he made fly across the field, each aiming at the original Pokémon. Mewtwo's Pokéballs capture them one after another, now leaving Pikachu. A dozen Pokéballs are sent to him. He runs, sometimes shooting an electric beam. Ash wants to be near him to help him. Finally, Pikachu is captured by a Pokéball. Panicked, he runs after it, but it flies away.

In the laboratory Team Rocket is in, Mewtwo's Pokéballs which contain the trainer's Pokémon are carried on the conveyer belt. As a mechanical hand takes one, the computer analyzes the gene, and creates a copy. Pikachu's Pokéball arrives, and Ash follows. As the hands are stretching toward it -- Ash seizes it tight in both his hands, as the hands reach it. Ash pulls with all his might, then hands grabbed him too. Ash gives another strong pull. Magic hands, which are on the Pokéball and him, are torn, sparking. The computer also breaks, and Mewtwo's Pokéballs spit Pokémon out. Pikachu is saved, and Ash hugs him tight in his arms.

Copies are summoned by Mewtwo and go to the field. Ash and Pikachu follow them with originals. Then they see a small, white Pokémon 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 the original Pikachu, and beats him hard. Pikachu doesn't resist and is hit by the copy's blow, and thrown away.

Pokémon, both originals and copies, fight, collapse, and fight... Only, Pikachu doesn't fight, though he is harshly beaten 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 where Mew and Mewtwo are fighting, crying, "Don't! Don't fight any longer!" Two Pokémon 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 shoots 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, Ash 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 float 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 Pokémon 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. No one remembers what happened on the island. The storm is over a moment later, and the sea recovers the peace, it's surface brightening in the sunlight.