Plot
Giovanni, leader of Team Rocket, recruits scientist Dr. Fuji to create a cloned supersoldier from an eyelash of the Mythical Pokémon Mew, with Fuji intending to use the research to clone 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 becomes traumatized after Ambertwo and the rest of the clones decompose and die. To stabilize him, Fuji tranquilizes Mewtwo, causing him to fall into suspended animation.
After Mewtwo fully matures and awakens from his long slumber in the laboratory on New Island, he learns of his origins. Infuriated that Fuji and his colleagues see him as a mere experiment, he uses his psychic abilities to telekinetically destroy the laboratory and kill Fuji and the scientists. Giovanni, witnessing the carnage from afar, offers Mewtwo his help to develop and perfect his mental abilities. However, after Mewtwo realizes his purpose as a weapon for Giovanni's benefit, he destroys Team Rocket's headquarters and returns to New Island, plotting to exact revenge against humanity and Pokémon alike.
After rebuilding the laboratory and establishing a base there, Mewtwo sends invites to several trainers through hologram messages to battle the greatest Pokémon Master in the world on New Island. Ash Ketchum, Misty, and Brock receive a message and accept the invitation, but by the time they arrive at the port city, Old Shore Wharf, Mewtwo has created a storm, causing the boats to be closed off for safety. To make it over there, Ash's group is 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 to reach New Island.
Escorted into the island's palace by the woman who appeared on the hologram, Ash and the other trainers who reached 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. Team Rocket, having also reached New Island, explore its inner sanctum, with 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 to 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 to prove his superiority.
All the Pokémon originals battle their clones, save for a defiant Pikachu and Meowth, the latter reconciling with his clone after realizing the senselessness of their fighting. Ash, horrified at the pain and anguish felt on both sides of the battle, puts himself in between a psychic blast caused by Mewtwo and Mew's fighting, which petrifies him. Pikachu tries reviving Ash with his electricity but fails, and he and the other Pokémon, original and clone alike, are reduced to tears. However, Ash is revived by these tears, and Mewtwo is moved by the boy's sacrifice, realizing that he and others should not have to be judged by their origins, but rather by their 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 events.
Back in Old Shore Wharf, the now-restored Nurse Joy reopens the Pokémon Center to shelter the trainers. As the storm outside clears up, Ash spots Mew flying through the clouds and tells his friends how he saw another legendary Pokémon the day he left Pallet Town for his journey. Meanwhile, Team Rocket find themselves stranded on a revitalized New Island, unable to remember how they got there, but enjoy their time nonetheless.
