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.