Liam's Adventures of Pokemon: Mewtwo Returns

Liam's Adventures of Pokemon: Mewtwo Returns is an animated mini-movie in the Liam's Adventures of Pokemon Series.

Plot
Mewtwo, its heart having been softened by the selfless example of Ash Ketchum back in the eastern Kanto 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 Mount 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 Mount Quena.

Ash and his friends—on their Pokémon journey as always—are passing through an area around Mount 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 Mount 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 Mount Quena, which Luna laments would bring tourists and destruction to the ecosystem.

Suddenly, 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 Mount 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 Mount 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 para-glider 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 Mount 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 jet-pack 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 Mount 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 Mount 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 Mount 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.

Major Events

 * Ash, his friends, and Team Rocket encounter Mewtwo again.
 * Ash, Misty, and Brock meet Giovanni for the first time.
 * Mewtwo erases its encounter with Giovanni, his underlings, Domino, Luna, and Cullen from their memories.

Trivia

 * This and Delibird's Dilemma take place sometime between The Grass Route! and A Ghost of a Chance, according to https://bulbapedia.bulbagarden.net/wiki/Timeline_of_events_in_the_anime