

After Ash was revived by the tears of the nearby Pokémon, clone and original alike, Mewtwo experienced a change of heart and no longer sought to conquer the world. Mew and Mewtwo fought at length, ceasing only when Ash-exasperated over the drawn-out and fruitless battling-ran into the fray and was caught in their crossfire, which turned his body to stone. However, before Mewtwo could defeat the Trainers and move out into the world, Mew appeared.

Once caught in the Balls, the Trainers' Pokémon were cloned in a downstairs laboratory. To do this, Mewtwo used a variation of the Poké Balls used by Trainers. Upon revealing itself, Mewtwo challenged the Trainers with its clone Pokémon- Venusaur, Blastoise, and Charizard-to prove its superiority to human Trainers and the superiority of cloned Pokémon in comparison to trained Pokémon. Only a handful of Trainers decided to brave the storm and arrive, including Ash and his friends. It used its powers to create a storm that would serve as a test to see who could make it to the island. Mewtwo then issued a challenge to several strong Pokémon Trainers, including Ash Ketchum. Mewtwo escaped from Giovanni, destroying Team Rocket headquarters in the process (something that the Team Rocket trio witnessed, ironically around the time they themselves considered defecting from Team Rocket), and relocated to its birthplace on New Island and built a castle there. It developed a strong hatred for humans and felt that they were weak and selfish beings who were only interested in power and wealth it also despised the Pokémon who served humans. Mewtwo eventually became tired of being used by Giovanni. At one point, Giovanni, after temporarily (at the time) abdicating the Viridian Gym to Jessie James and Meowth, utilized Mewtwo for what was presumably a very serious matter. Mewtwo's power was focused as well as restrained by a robotic suit of armor as it performed tasks, such as battling for Giovanni in the Viridian Gym and helping Team Rocket capture Pokémon. Immediately thereafter, Giovanni found Mewtwo and convinced it to help with Team Rocket's goal of controlling the world.

Despite the efforts of the security systems that were designed to control it, Mewtwo destroyed the laboratory on New Island and all of the scientists in it. Realizing that it was just an experiment of mankind, Mewtwo unleashed its fury upon them. The Team Rocket scientists were happy that they had succeeded in creating the most powerful Pokémon in the world, but that joy turned to horror once Mewtwo retaliated. After resolving to figure out where it belongs, Mewtwo broke out of its tank, with Mewtwo exchanging some words with its creators while asking about the nature of its existence and its destiny. Over the years, Mewtwo matured and grew confused over its origin and place in the world. Before this, Mew was revealed to have an immortal life force, explaining why Mew's DNA sample made a successful clone in Mewtwo. However, because the cloning process requires a strong life force, all four other clones died. Fuji and the other scientists thought that Mewtwo was unconscious inside its tube, but it was able to communicate telepathically with Ambertwo and the other clones. At this point, it was still not fully grown and lived in a large tank beside others that contained Bulbasaurtwo, Squirtletwo, Charmandertwo, and Ambertwo. One month after the discovery of the eyelash, Mewtwo was successfully created and stored at New Island. Fuji agreed, but only in order to continue his research into cloning his deceased daughter, Amber. Fuji to clone Mew for him and create the most powerful Pokémon in existence. Many years later, under the orders of the new boss Giovanni, an expedition team of Team Rocket scientists traveled to the area to search for a fossil of Mew, and succeeded in finding an eyelash belonging to it. Approximately twenty years ago, Team Rocket discovered that a Mew was living in Guyana.
