In the Pokémon universe, Tim Goodman is a 21-year-old insurance agent who surrendered his fantasy about being a Pokémon trainer following the demise of his mother and becoming antagonized from his father Harry Goodman. Tim is reached by the police of Ryme City, a city where people and Pokémon live respectively in agreement, and thusly, catching and battling with Pokémon is banned. He is informed by Harry's companion and Ryme City police criminologist, Hideo Yoshida, that Harry was murdered in a fender bender.
Tim goes to Harry's loft to sift through things and meets a deerstalker-clad Pikachu that can talk and be comprehended by him, however all others essentially hear him state "Pika." Tim unintentionally discharges a puzzling purple gas, "R," from a vial he finds in Harry's office; they are then assaulted by a gathering of Aipom[d] who become frenzied under the gas' influence.
The pair getaway and Pikachu explains he has amnesia and his solitary sign to his character is Harry's name and address on his top, leading him to accept he was Harry's accomplice and that Harry endure the accident. They meet an informant of Harry's, a Mr. Emulate who guides them to an underground unlawful Pokémon fight field. The field's proprietor, Sebastian, perceives Pikachu, who had injured his Charizard in a past fight, and requests a rematch. He dosages Charizard with the purple gas, stirring it into a brutal fierceness and Pikachu can't bring his electrical forces to retaliate. While attempting to spare Pikachu, Tim thumps Sebastian over and breaks a few gas vials in his coat, sending the field's Pokémon into a free for all. The field is assaulted by police and Tim is brought to Lieutenant Yoshida, who uncovers film of Harry's accident. Using the recording as proof, Yoshida reveals to Tim that it is unthinkable for Harry to have endure the accident. In any case, Tim still chooses to seek after the secret of how Pikachu lost his recollections.
Tim and Pikachu are reached by Howard Clifford, the wheelchair-bound originator of Ryme City and organizer of Clifford Industries. Howard uncovers Harry endure and was taken by a propelled type of Mewtwo, who deleted Pikachu's memory. He cautions Tim that his child Roger is behind the making of "R", and in the event that he finds Mewtwo, he can find his father. Tim and Pikachu select aspiring columnist Lucy Stevens and travel to the relinquished hereditary qualities lab Harry was investigating. The lab's work force had been experimenting on Mewtwo and synthesized "R" from its qualities. They are assaulted by hereditarily improved Greninja and Pikachu is gravely injured. Tim asks a Bulbasaur to support his Pokémon and it drives him to Mewtwo, who recuperates Pikachu before being caught by Roger. Pikachu recalls that he helped Mewtwo escape from the lab and accepts he was answerable for betraying Harry. Not trusting himself, he leaves Tim.
Pikachu runs over the location of the fender bender and finds proof that it was the Greninja, not Mewtwo, who were mindful. In Ryme City, Howard uncovers the caught Mewtwo to Tim, exposing himself as the genuine mastermind: he assumes responsibility for Mewtwo's body using a neural-link protective cap that puts his mind inside Mewtwo's while his human body remains in the wheelchair. He explains that Mewtwo can combine people and Pokémon, allowing people to develop as Pokémon can and get one with them, yet this must be done if the Pokémon is in a confounded state, consequently the requirement for "R". This likewise implies handicaps like Howard's won't exist. Believing this is the fate of humankind, Howard discharges the gas over the city and begins fusing people with their Pokémon. Pikachu gathers his electrical forces to fight Mewtwo while Tim battles Howard's hereditarily altered Ditto, who had been impersonating Roger; the genuine Roger had been tied up and choked by his father. Tim figures out how to expel Howard's protective cap from his body, freeing Mewtwo from his control.
Mewtwo reestablishes the city inhabitants to ordinary, Howard is captured and Roger employs Lucy as a full-time journalist, promising the city that he will fix his father's errors. Mewtwo explains that Harry attempted to spare him from Howard and aided Mewtwo escape, however was assaulted by the Greninja. Pikachu had elected to have himself melded with Harry to spare his life, the experience erasing both their recollections. Mewtwo isolates the two and Harry reunites with Tim in his human body. Tim chooses to remain in Ryme City to turn into an investigator and invest more energy with his father and Pikachu.
Mewtwo reestablishes the city inhabitants to ordinary, Howard is captured and Roger employs Lucy as a full-time journalist, promising the city that he will fix his father's errors. Mewtwo explains that Harry attempted to spare him from Howard and aided Mewtwo escape, however was assaulted by the Greninja. Pikachu had elected to have himself melded with Harry to spare his life, the experience erasing both their recollections. Mewtwo isolates the two and Harry reunites with Tim in his human body. Tim chooses to remain in Ryme City to turn into an investigator and invest more energy with his father and Pikachu.