Pokémon Mewtwo Returns is the first feature-length special of the Pokemon anime. It was first broadcast in Japan on December 30, 2000. It was then released on DVD in the US on December 5, 2001.
Mewtwo, the legendary its heart having been softened by the selfless example of Ash Ketchum back in the easternKanto region, has now traveled to the western region of Johto in search of a place unreachable to the prying eyes and harsh judgments of humans for the sake of the band of cloned Pokémon, whose welfare Mewtwo is entirely concerned with. Mewtwo eventually finds the perfect hideaway: a huge mountain named Mount Quena, surrounded by steep cliffs that are practically impossible to scale, but in its crater is a freshwater lake and a forest that is home to many Bug Pokémon. This is a perfect fit for Mewtwo's band, so they settle in the top of Mt. Quena and begin a new, safe life. Mewtwo, feeling that clones do not belong in the outside world because they were not born in it, watches over as their guardian. Mewtwo seems particularly close to the Pikachu and Meowth clones, spending most of its private time with them, possibly reflecting how important their templates were in its change of heart.
Giovanni however, is determined to possess Mewtwo once again, and has been planning a militaristic assault upon wherever Mewtwo has settled to take the Pokémon back for himself. He at last locates Mewtwo in its new mountain retreat, so the Team Rocket Combat Unit heads toward Mt. Quena.
Ash with his friends—on their Pokémon journey as always—are passing through an area around Mt. Quena called Purity Canyon, which is known as Johto's greatest natural wonder. Unfortunately, they miss the only bus that goes through the area and an unpredicted typhoon forces them to stay at a lodge at the foot of the mountain with a woman who could not board the full bus. On the road, the bus is swept up high powerful winds, but is set down by Mewtwo's powers, much to the confusion of its riders. In Mewtwo's lair, Pikachutwo questions this action, which Mewtwo explains was to prevent rescuers from jeopardizing the clones' seclusion. Meowthtwo suggests it may also have been done out of compassion, of which Mewtwo says it has none for humans.Back at the lodge, Pokémon naturalist Luna Carson explains that the only ways through the valley are a canoe ride down the river or the monthly bus service. Later, Luna serves them fresh water from Purity River, and everyone but Ash is amazed by its taste. With no other option for transportation, the group leave that night, taking the canoes downstream. Along the way, they come across the Bug Pokémon Ledian, Kakuna, Weedle, Pinsir, and Beedrill, the last of which causes Misty to frantically paddle back upstream. Back at the lodge, Brock suggests they scale Mt. Quena, but Luna warns that is impassible despite featuring beautiful Clarity Lake in its crater. A knock on the door brings new lodge inhabitants: medical researcher Cullen Calix and a spunky girl from the Pokémon Institute, Domino. Cullen says he is studying the medicinal properties of Purity River water and wants to explore Mt. Quena, which Luna laments would bring tourists and destruction to the ecosystem.
Suddenly the evil Team Rocket announces their presence with firecrackers and their motto. James grabs Pikachu with an electricity-absorbing whip and escapes with Jessie, and Meowth in their rocket-powered balloon, but the turbulent winds cause them to lose control and push them toward Mt. Quena. The group equips climbing gear and chases after them, avoiding gusty winds and even a falling boulder. Team Rocket's balloon swings by and hooks their climbing rope, dragging the group into the air. Domino spots Mewtwo in Mt. Quena through her binoculars and transmits a video feed to none other than Giovanni. Upon seeing the approaching Combat Unit, Domino climbs up the rope past the others, lands in the balloon's basket, and reveals herself to be in league with Team Rocket as elite Agent 009, also known as The Black Tulip for her use of the flowers as weapons. Domino pops the balloon with one and sends everyone else plummeting onto the mountain while she returns via paraglider to Giovanni's large helicopter to report on Mewtwo's status.
Pikachu and Team Rocket end up separated from the others and quickly encounter the clones. Pikachu's clone attacks Pikachu for suddenly appearing, but Mewtwo forces it to stop. Agitated by the approaching humans, Pikachutwo rallies the other clones to fight back against the invading Combat Unit. Mewtwo stays behind with other clones and contemplates whether to stop the fighters from endangering themselves or letting them act freely. Ash and the other humans land unharmed, but separated from Pikachu by a lake. They use Bulbasaur and Chikorita's Razor Leaf to make a canoe and oars out of a fallen tree, and with it they traverse the lake to reach the island at the center of Mt. Quena's crater. They enter a natural sanctuary in the island, where Cullen discovers that the water inside could have a profound impact on medicine. Luna fears that any future human presence could taint the purity of the water and destroy the habitat.
Some of the clones imprison Jessie and James in a cave and head off with Pikachu and Meowth to fight Team Rocket's forces. However, as soon as the Pokémon land ashore, a Team Rocket helicopter appears and stuns the clones with energy blasts. An airship drops Team Rocket Poké Balls that capture most of the clones, and just as Pikachutwo is about to be caught by one, Pikachu deflects it with an electric attack. He also shocks Pikachutwo in order to invigorate it and escape, which Meowth emulates by scratching Meowthtwo's face. The four Pokémon flee from the helicopter's blasts, but find themselves trapped against a hill. A Shadow Ball saves the group from an incoming stun blast, revealing Mewtwo floating in the air behind the helicopter. Mewtwo frees the clone, disintegrates their Poké Balls, and throws another Shadow Ball, but the helicopter evades the attack.
Giovanni emerges on a platform to speak with Mewtwo, but the Pokémon refuses to go along with Giovanni's plans. The helicopter deploys two machines that surround Mewtwo and give it a powerful electric shock. Mewtwo pushes the machines into rock walls with its psychic power and defies Giovanni once more. Giovanni turns his attention to the island harboring the rest of the clones for phase two of the operation. Along with paragliding Team Rocket Grunts, Domino flies over using a jetpack and eventually comes across Ash's group, who are quickly restrained by metal rings to prevent their interference. Domino subdues the island's Pokémon with stunning tulips and restraining rings and reports her findings to Giovanni, who challenges Mewtwo to stop him. Mewtwo declares that it will protect the clones and telekinetically brings the other Pokémon to the island with it.
Soon, Domino, Mewtwo, and Giovanni meet on the island, at which point Giovanni tells Mewtwo that it must surrender. Mewtwo replies that it would rather leave this world than serve him, but Giovanni threatens to subject the other clones to experiments that would cause them to perish. Mewtwo then agrees. Giovanni reactivates the machines from earlier and tells Mewtwo to enter the energy field between them, which will harness Mewtwo's power and bend its will to his. Domino demonstrates Team Rocket's threat by firing blasts from her tulip at Pikachutwo. With Mewtwo trapped by the force of the machines' energy and his operation successful, Giovanni makes plans to build a Team Rocket laboratory on the island to create an army of powerful clone Pokémon. Mewtwo ceases its struggle just as Giovanni states that it will be his tool to rule the world. The other characters and Pokémon are then locked away in a prison cell, where Ash is reunited with Pikachu.
Outside, construction is well under way on the Team Rocket base. In a phone call, Giovanni tells Domino that Mewtwo's brain waves are resisting the machine's influence at a rate that would destroy its body before giving in. The industrial waste from the base attracts the ire of Mt. Quena's resident Bug Pokémon: hundreds of Ledian, Butterfree, and Beedrill, whose lake water is now polluted. When the welders inside the facility are taken out by Butterfree's Sleep Powder, a dropped blowtorch ignites the fuel cells below and causes enormous chain explosions, one of which destroys the cell bars and frees the human and Pokémon prisoners. Luna and Cullen head toward the spring to check its purity.Domino throws black tulips at a group of Ledian, but several Scyther slice the weapons up. She then uses a rod-like tulip to fend off an attacking Scyther and vault over the Ledian swarm. After being forced to mop the floor earlier, Jessie and James enjoy Domino slipping and falling head-first into a bucket of water.
Ash, Pikachu, Misty, Brock, Pikachutwo, Meowth, and Meowthtwo find Mewtwo. Everyone but Misty tries to free Mewtwo by tackling one of the machines, but it only tips over and maintains the energy field. Mewtwo resorts to using the last of its power to overload the machines. Pikachu and Pikachutwo use Thunderbolt on one of them, which explodes. The field breaks, and Mewtwo collapses to the ground. The other machine appears to malfunction and self-destruct. Before they can take Mewtwo to the spring to recover, Giovanni appears with Team Rocket and claims that Mewtwo belongs to him. Brock and Misty release all their Pokémon to fight, and the clone and Bug Pokémon show up as well. Meowth flees the scene with Jessie and James while Ash takes Mewtwo away by himself.
As Ash, Bulbasaur, and Chikorita transport Mewtwo to safety, Mewtwo asks why Ash is helping it. Ash replies that Mewtwo saving Pikachu is one reason, and at Mewtwo's questioning, goes on to say that you do not need a reason to help someone in trouble. Mewtwo reflects that Ash may be one-of-a-kind, but Ash says that everyone is. They reach the heart of the mountain, and despite Cullen's protests that Mewtwo may contaminate the spring, Ash throws Mewtwo in because it needs the water's healing power most. Since the water heals it like it does other Pokémon, Mewtwo realizes that it does belong in this world. A blast from a helicopter announces Giovanni's sudden presence, but a rejuvenated Mewtwo rises from the water to protect the land it calls home. Mewtwo causes a great blue light to shoot up from the entire lake and pierce the heavens.Night has fallen, and Team Rocket wake up from unconsciousness in a dry crater. Underground, Mewtwo explains to the other humans that it has moved the lake and spring inside Mt. Quena for greater protection. When Mewtwo decides to erase the memories of everyone involved, Meowth and the other Pokémon object, arguing that the past forms part of a living creature's identity and it is entitled to it. Misty and Brock add that forgetting the past does not change it and everyone deserves to know where they came from. Mewtwo changes its mind, stating that we should be able to look to the past just as much as the future, and the shame of others' wrongdoing is theirs alone. A group of Butterfree spread powder enhanced with Mewtwo's psychic abilities to erase the memories of the Team Rocket operatives as well as Luna and Cullen, whose well-meaning desire to research the spring may put it in jeopardy. Like the Team Rocket trio before them, Ash and his friends board a Pikachu balloon to leave Mt. Quena. Mewtwo earnestly thanks them for their help and departs with all the cloned Pokémon to live elsewhere as natural Pokémon in the wild.Some time later, as Ash, Misty, and Brock walk through a city, Ash hears Mewtwo's voice, but is uncertain whether it was real or just a memory. The Narrator concludes the movie with the rumors of a Pokémon who traverses a faraway city at night.
Ash Ketchem is rereading his letter, inviting him to Dr. Yung's lab, to Brock, May, and Max. When he gets there, he is shocked to see Misty and Professor Oak. Dr. Yung appears, and shows them a few mirage Pokémon. He invites Misty to battle one. Misty sends out her Staryu against a mirage Aggron. She is shocked that Staryu's most powerful attacks don't even make it blink. Staryu goes out quickly. Ash begins to battle when an Armaldo suddenly locks up. Yung's Mirage Pokémon System has mysteriously locked up! The controller explodes in his hands, and a handful of legendary Pokémon appear. A stranger, calling himself Mirage Master, uses the system he has just hijacked to his advantage, kidnapping Professor Oak and Dr. Yung. Ash and his friends cannot get back inside because a bunch of mirage Pokémon stand just inside.Oak, in the custody of Mirage Master, demands to know where Dr. Yung is. Mirage Master ignores his query, and demands the password to Professor Oak's research lab. Oak refuses while a Mew flies in. Professor Oak is greeting it when Mew is attacked. The Professor demands to know why Mirage Master did that. The Mirage Master says that Mew was a failed creation, and he tells Mew to leave.Ash, Misty, Brock, May, and Max formulate a plan. Ash and Misty will sneak in through the moat, Brock will alert Officer Jenny (with the intention of receiving a candlelight dinner for two), and May and Max will wait in case Ash and Misty get in trouble. They split up. Ash and Misty use Corphish and Staryu to get in.
Team Rocket, after the Mirage System Plans, are looking around. They attempt to burst through a door, only to have it hit them in the noses! Ash and Misty walk through, Team Rocket does the motto, thereby wasting enough time for Mirage Master to check the camera and send in mirage Pokémon. Team Rocket escapes, Ash, Misty, and Pikachu are held by two mirage Machamp and a mirage Ursaring. As the three are being carried, Ash sees Mew appear again, and Pikachu uses Thunderbolt. Some various things are blown up, including a wall, signaling to May and Max. May goes in, and tells Max to wait. Pikachu frees all of them, Misty falls over the edge of the bridge, and Pikachu is recaptured, leaving Ash and Mew. Mew is suddenly trapped by a force field, and Ash manages to get Mew free. Ash discovers that Mew is a mirage Pokémon. Pikachu is in a fearsome-looking device. Professor Oak asks what the Mirage Master is doing. Mirage Master says he will extract Pokémon data from Pikachu's memory, and that this would not be needed if Oak was cooperative. Pikachu contorts with pain. He looks at the picture displaying Pikachu's memory. Lugia... Entei... Celebi... Latios... Latias... These are all rare Pokémon Pikachu has seen. Oak cannot stand the look of Pikachu, and enters in the password: REDGREEN. Suddenly, Mirage Master has the ability to download information from places around the world. Tracey and Professors Elm and Birch stare at computers in their labs, while Nurse Joy deals with problems at the Pokémon Center.
"You have to believe me, Officer!" Brock pleads to Officer Jenny. "We need to go to Professor Yung's lab for a candlelight dinner... I mean-" Nurse Joy flickers onto the officer's computer. She tells the officer that someone is downloading massive amounts of Pokémon data. Brock tells her about Mirage Master, and they leave.
Misty is hanging onto the edge of a bridge. She suddenly loses her grip, and May appears in the nick of time to save her. They go upstairs. Ash and Mew are there already, and the process of creating the Pokémon finishes in a flash of light. A mirage Mewtwo emerges. He attacks them, and they run. Outside of the boundaries of the Mirage System, the heroes think they are safe. Then, missiles are launched from the towers, and they expand the system! Mewtwo and Mirage Master emerge. Mirage Entei, Articuno, and Zapdos suddenly appear. Oak correctly guesses the identity of the Mirage Master. Mirage Master removes his mask, revealing Dr. Yung! Oak reveals that when Mirage Master first appeared, he was a hologram, and that Yung was expelled from the Pokémon Institute for his research, deemed disrespectful to Pokémon. Yung's Mewtwo and Ash and company battle. Yung is about to obliterate Pikachu when Mew takes the blow. Mew then is absorbed into the Mirage System. Yung says "good riddance," and Mewtwo absorbs the entire Mirage System database. Ash is enraged that Mew is called a failed creation, and the attack begins anew.
Team Rocket is blown away in this fight. Pikachu is about to be killed when Mew holds Mewtwo back! Ash orders Pikachu to perform Volt Tackle, and Mewtwo is destroyed, as are Mew and the System. The fortress is now aflame, and Yung retreats inside. The police are searching, as are firefighters, but they cannot find him yet. The gang discusses what happened, and agree that Mew was far more than just data and certainly not a 'flawed specimen' as Yung believed.