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Tim and Pikachu are contacted by Howard Clifford, the founder of Clifford Industries and creator of Ryme City. Howard reveals that Harry was abducted by a genetically engineered Pokémon called [[Mewtwo]], who erased Pikachu's memory of the incident. He warns Tim that his son, Roger Clifford, is behind the creation of the R gas. Tim and Pikachu recruit aspiring journalist Lucy Stevens and her [[Psyduck]] and travel to the abandoned genetics laboratory Harry was investigating, where they are attacked by genetically enhanced [[Greninja]]. They manage to escape, but Pikachu is injured in the attack. A [[Bulbasaur]] leads them to Mewtwo, who heals Pikachu and begins to reveal how Pikachu helped him escape from the lab, only to be abducted by Roger mid-revelation. Believing himself to have betrayed Harry, Pikachu leaves Tim.
Pikachu discovers the scene of the crash and finds evidence that the Greninja, not Mewtwo, were responsible for the crash. Back in Ryme City, Howard reveals himself as the true mastermind behind the "R" gas and the Mewtwo experiments. He explains that Mewtwo can fuse humans with their Pokémon, but only if the Pokémon is in a crazed state, thus necessitating the need for R. Howard uses a device to transfer his consciousness into Mewtwo, unleashes the gas on the city from parade balloons and starts fusing humans with Pokémon, including Lucy and Yoshida. Pikachu arrives and fights Mewtwo, while Tim discovers that Roger, who appeared to be working in tandem with his father, is really Howard's genetically modified [[List of generation I Pokémon#Ditto|Ditto]]; the real Roger was tied up and gagged to complete the deception. They eventually defeat Howard by removing the headset on his head, freeing Mewtwo from his control. Mewtwo separates the people and their Pokémon, Howard is arrested, Roger vows to undo his father's misdeeds and Lucy is tasked with spearheading the media coverage.
Mewtwo explains that Harry had tried to save him from Howard and helped Mewtwo escape, but was attacked by the Greninja. Mewtwo then decided to heal Harry's wounded body, which was when Pikachu volunteered to have his consciousness fused with Harry's in order to continue their investigation, and as a result, the experience erased both Harry's and Pikachu's memories. Mewtwo separates the two, and Tim reunites with his father in his human body. Tim then decides to stay in Ryme City to become a detective and spend more time with his father, Pikachu, and Pokémon.
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