The Pokémon Mewtwo was created in an island laboratory from the DNA of Mew, a rare Pokémon believed to be extinct, recovered from fossilized remains. Displeased with the concept of being nothing more than a mere lab experiment, Mewtwo destroys the laboratory. Shortly afterward, he meets Giovanni, the head of Team Rocket, who proposes a partnership with the Pokémon in exchange of helping him control his powers. Mewtwo is "trained" over the next few months, being pitted against challengers in Giovanni's gym and restraining Pokémon for Team Rocket to capture. Mewtwo eventually realizes that Giovanni is merely using him as a tool and destroys his headquarters. After defeating Giovanni, Mewtwo flies back to the island where he was created and begins plotting revenge against humanity.
Meanwhile, Ash Ketchum and Pikachu compete against a Pokemon trainer. Pikachu's thundershock gets the attention of Hubie, Marina, Rocko, Petra, Beanie and Timmy who have left Antarctica to begin their own travels. They reunite with Ash, Pikachu, Misty, Brock and all their Pokémon companions and join them for lunch. Later, they receive an invitation to a party hosted by the world's "greatest Pokémon Master" on New Island. Ash and his friends are excited and invite Hubie and his friends to join them. They agree and rush to the docks in an attempt to catch a boat to New Island, but a storm is mysteriously formed and all boat rides to the island are canceled and the Pokemon Center nurse has gone missing, in which a toon cop named Bonkers D. Bocat has been trying to find. Undeterred, several trainers make their way out to the island by riding their Pokémon, though neither Ash nor his friends have any Pokémon of their own that can help them safely navigate the stormy sea. In their latest plot to steal rare Pokémon, Team Rocket offers the trio a lift to the island, disguised as a pair of vikings, but their small wooden boat is destroyed by a wave. Ash, Hubie and their friends manage to reach the island with their aquatic Pokémon, and are escorted inside the palace on the island. Bonkers has joined them too, suspecting that Nurse Joy is on the Island.
Mewtwo reveals himself to Ash, Hubie and their friends, and three other trainers who braved the storm battle as the "World's Greatest Pokémon Master," and that it had created the storm with its powers to test the trainers' wills. After being berated by Mewtwo for the relationships they share with their Pokémon, Ash and some of the other trainers challenge Mewtwo after witnessing Mewtwo's confession of having kidnapped Nurse Joy for his own personal purposes. The trainers pit their Pokémon against clones of Venasaur, Charziard and Blastoise. The clones easily defeat the Trainers' Pokémon. Mewtwo proceeds to steal all the Pokémon present, including Ash's Pikachu, with a special set of Poké Balls. Ash pursues his Pokémon along with Hubie as they are taken deep into a cloning facility on the island and rescue them while they are being cloned. The clones join with Mewtwo and the cloning machine explodes, releasing all the captured Pokémon. Mewtwo announces his intentions to overthrow humanity with his army of Pokémon.
Enraged, Ash and Hubie lash out at Mewtwo, who repels and blasts them both him away with his psychic powers. But they are saved by Mew, the rare, playful Pokémon having appeared periodically before, who is engaged by Mewtwo. A brutal battle between the Trainers' Pokémon and their clones erupts, although Pikachu refuses to fight with his own clone resorting to slapping it (Meowth's clone also seems to refuse to fight, causing the original Meowth to ponder on what the two sides have in common).
The trainers, Marina and the others are unable to bear this senseless violence, even while Mew and Mewtwo grow tired but continue fighting. In an attempt to put an end to the ordeal, Mew and Mewtwo sum up all their remaining powers for one final duel. Marina even runs in to protect both Pikachu and its clone. However, just as Mewtwo and Mew open fire, Ash and Hubie run to the center of the arena in a brave but desperate attempt to stop the fight. Both Mew and Mewtwo's attacks hit Ash and Hubie at the same time, turning them to stone after they sink onto the floor.
Pikachu runs to Ash's side and tries to wake him up. He uses Thunderbolt on Ash, while the other Pokémon, Rocko, the birds, Bonkers, Brock, Misty, and Nurse Joy look on. After several vain attempts to revive Ash using Thunderbolt, Pikachu grows tired and stops. Marina, realizing that Hubie is dead, collapes over his stone body and breaks down in tears. Pikachu starts crying for Ash, the other Pokémon in the arena doing the same. Their tears all gather together and eventually reach Ash and Hubie, their mystical healing powers bringing them back to life. Overjoyed, Pikachu leaps into Ash's arms as the two embrace, as do Hubie and Marina, (sharing a kiss) happy to be reunited once again.
As everyone rejoices, Mewtwo, taken aback by Ash and Hubie's act of selflessness and love to save all the Pokémon, has an epiphany over the relationship between humans and Pokémon, and realizes that the circumstances of how one is born should not be allowed to divide anyone. He leaves the island with Mew and the cloned Pokémon, erasing everyone else's memory of the horrifying incident, knowing it is for the best.
Ash and his friends find themselves back on the docks with no idea how they got there. Ash looks up to the sky and spots Mew flying past, and recounts to his friends how he saw a rare Pokémon on the first day of his journey.
Meanwhile, Hubie, Marina and their friends find themselves at a beach, along with Bonkers. Hubie offers Bonkers to join him and the others on their journey and he agrees with delight.
Part 1: https://vimeo.com/87433048
Part 2: https://vimeo.com/87558339
Part 3: https://vimeo.com/87926233
Part 4: https://vimeo.com/87977392
Part 5: https://vimeo.com/88504883
Part 6 & Credits: https://vimeo.com/88810911
- This film actually takes place after Ash's Adventures of The Pebble and The Penguin, which explains Hubie and his friends already knowing Ash and his friends.
- Bonkers joins the team.