The Pokémon of Ash Ketchum, Misty, and Brock are sent to spend a day at a theme park built for Pokémon. Pikachu, Togepi, Bulbasaur, and Squirtle cross paths with a group of bullies consisting of a Raichu, Cubone, Marill, and a Snubbull. The two groups compete against each other in sports, but it leads to Ash’s Charizard getting its head stuck in a pipe. Pikachu, his friends, and the bullies work together and successfully free Charizard and rebuild the park, spending the rest of the day playing before parting ways when their trainers return.
Mewtwo Strikes Back
Scientist Dr. Fuji is hired by Giovanni, leader of Team Rocket, to utilize his expertise in cloning in order to create a living weapon based on an eyelash from mythical Pokémon Mew. Fuji is revealed to be allying with Giovanni as a means to fund his side project: the resurrection of his deceased daughter Amber. In a laboratory, the weapon eventually gains sentience and is named Mewtwo. Mewtwo befriends the salvaged consciousness of Amber, named Ambertwo, as well as the clones of other Pokémon in the laboratory. However, Mewtwo is left deeply traumatized after Ambertwo and the rest of the clones decompose and die. In order to stabilize him, Fuji tranquilizes Mewtwo, causing him to forget the time he spent with his friends.
After Mewtwo fully matures and awakens from a long slumber in a laboratory on New Island, he learns of his origin as Mew’s clone from Dr. Fuji. Infuriated that Fuji and his colleagues see him as nothing more than an experiment, he unleashes his incredibly strong psychic abilities and telekinetically destroys the laboratory, killing Fuji and the rest of the scientists. Giovanni, witnessing the carnage afar, approaches and convinces Mewtwo to work with him to further develop and perfect his mental abilities. However, after Mewtwo learns of his purpose to be a weapon for Giovanni’s benefit, he escapes back to New Island where he plots revenge against humanity and Pokémon alike.
After Mewtwo rebuilds the laboratory and establishes base there, he invites several trainers with hologram messages to battle the world’s greatest Pokémon trainer at New Island. Ash, Misty, and Brock receive a message and accept the invitation, but when they arrive at the port city, Old Shore Wharf, Mewtwo creates a storm, causing the boats on the wharf to be closed off for safety. As a result, Ash’s group are picked up by Team Rocket disguised as Vikings on a boat. After the storm sinks their vessel in the middle of the ocean, Ash and his friends use their Pokémon instead to reach New Island.
Escorted into the island’s palace by the woman who appeared on the hologram, Ash and the other trainers who were able to reach the island encounter Mewtwo. The woman is revealed to be a brainwashed Nurse Joy after she is released from Mewtwo’s mind control. Mewtwo challenges the trainers using cloned Pokémon coincidentally modeled after the deceased friends from his childhood. Meanwhile, Team Rocket also reach New Island and explore its inner sanctum with a Mew innocuously following them. After Mewtwo’s clones effortlessly defeat the challengers’ Pokémon, he confiscates them and expands his clone army. Ash chases after his captured Pikachu down the cloning lab, where Team Rocket’s Meowth is also cloned. Ash destroys the cloning machine, frees the captured Pokémon, and leads them to confront Mewtwo and his clones. Mew then reveals itself and Mewtwo challenges it in order to prove his superiority.
All of the Pokémon originals battle their clones save for a defiant Pikachu and Meowth, who makes peace with his own clone after realizing the senselessness of their fighting. Horrified at the pain and anguish felt on both sides of the battle, Ash puts himself in between a psychic blast caused by Mewtwo and Mew’s fighting, leading to Ash to become petrified. Pikachu tries to revive Ash with its electricity but fails. However, the tears of the Pokémon are able to heal and revive Ash. Moved by Ash’s sacrifice, Mewtwo realizes that he should not have to be judged by his origins but rather his choices in life. Departing with Mew and the clones, Mewtwo turns back time to just before the trainers leave Old Shore Wharf, and erases everyone’s memories of the event.
Back in Old Shore Wharf, the now-restored Nurse Joy has returned to reopen the Pokémon Center to shelter the trainers. The storm outside clears up, Ash spotting Mew flying through the clouds and tells his friends of how he saw another legendary Pokémon the day he left Pallet Town. Meanwhile, Team Rocket find themselves stranded on New Island but enjoy their time there.
After the credits, a brief scene shows Mew flying towards the mountains.