Mewtwo starts life in a laboratory. He opens his eyes for the first time to see scientists all around him. The scientists created him, by using cells from Mew, who is the rarest Pokemon in the world, to create Mewtwo who is now the strongest of all Pokemon. Mewtwo realises that he was artificially created and in confusion, destroys the lab. The boss of Team Rocket, Giovanni, takes him and uses him to help him catch Pokemon. Meanwhile, Ash is waiting for Brock to serve up dinner at a table, overlooking the sea. Togepi again wanders off, and Pikachu saves him. A man challenges Ash to a match and he accepts. Ash eventually wins and his opponent gives him an invitation card, telling him to join a Pokemon League in the Pokemon castle on New Island. Ash accepts this invitation.
Ash makes his way to the port to get a boat to the Island, only to find other Trainers who had been invited to the castle. The sea is rough and so a boat cannot be launched, so the other Trainers use their Pokemon to fly or swim to the Island. Ash doesn't have a strong enough water Pokemon, but luckily a boat appears, and the owners offer them a ride. Ash and his friends get on the boat, relieved. During the voyage, a wind blows the hats off the boat owners revealing them as Team Rocket! A big wave hits the boat and everyone is thrown into the water. Ash and his friends use their Squirtle and Starmie to make the rest of the journey to the New Island.
A woman appears to tell all the Trainers to call out their Pokemon, which they do, surprised. They then see the host, who is Mewtwo. He tells them he is a Pokemon trainer and some of the other Trainers become enraged because he is only a Pokemon. They send some of their Pokemon to fight Mewtwo, but he wins easily. He takes all the Trainers to a league field, which he constructed himself. Meanwhile, Team Rocket make their way into the castle and by accident, into a lab. Meowth is then captured by some mechanical arms. They pluck hairs from him, and a computer gets all of his genetic details. A clone of Meowth is then created, which is stronger than the original. Team Rocket find out that it was Mewtwo who did this. Other Pokemon clones appear and go to the league field, called by Mewtwo by telepathy.
Mewtwo knows what Pokemon all of the Trainers have, and says he will prove to them that his clones are stronger, which he does. Mewtwo then uses balls of energy to weaken all the original Pokemon, then captures them all in balls, leaving just Pikachu. Mewtwo eventually captures Pikachu, who puts up a struggle. The Pokeballs fly to Mewtwo's lab, and make copies of all the new Pokemon, except Pikachu who is rescued by Ash. The new copies go to the field and Ash and Pikachu follow them. They see Mew there, who is Mewtwo's mother. Mewtwo is upset and confused and starts to fight Mew. All of the original and copied Pokemon do the same, including Pikachu and his clone.
Ash is disgusted by the whole thing and runs over to Mew and Mewtwo to stop them fighting, but they each release balls of energy which hit Ash. He screams and collapses. All the Pokemon freeze and Pikachu runs over to Ash. His body stiffens. Pikachu shocks Ash, thinking it will wake him up, but it doesn't. He keeps trying, but gives up. Pikachu and all the other Pokemon start crying and their tears soak into the soil and over to Ash's body, which make him move slowly. Pikachu hugs him, and Ash hugs back. Mewtwo calls all the clones back. He believed that life was worth living after all, and after when Ash recovered, they left the Island and forgot all about it. The storm clears, reavealing the sunlight shining on the surface.
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