Mewtwo Returns (Part 3)

Mewtwo Returns (Part 3) (ミュウツー！我ハココニ在リ) is the third part of the special Mewtwo Returns.

Plot
After some of the ending events of the previous part are showcased, and after the title card, the part continues with more of the story. Ash and his friends, as while of the clones are inside the prison cell within the secret base. With Ash and the Pokémon Clones in custody, Giovanni's operation is successful, and he immediately capitalizes by ordering the construction of a new Team Rocket base on the mountain.

The characters and all other cloned Pokémon that attempted to protect Mewtwo are then locked away in a prison cell, along with two mother Pokémon attempting to protect their offspring. While in the cell Meowth translates what the other Pokémon are saying: They're coming...and they're very angry. They're mad at whoever is polluting the lake and they've come to stop them. Domino eventually releases Jessie and James and puts them to work cleaning the new base.

Giovanni's greed for new Team Rocket bases becomes his worst mistake; without warning, a swarm of furious Bug Pokémon (that Meowth was referring to) from the mountain sabotages the Team Rocket base that is polluting the freshwater lake, and the ensuing chaos allows Ash and everyone with him to escape and scatter. Ash rushes over to Mewtwo, believing that this is the first time he's seen Mewtwo, and he and Brock try to free Mewtwo from the machines that are suppressing his mind and body, partly as thanks for Mewtwo protecting Pikachu earlier. However, Mewtwo is weak from using what was left of his power and strength to destroy the machines that held him, putting his life force in jeopardy, but Ash carries Mewtwo away from Giovanni's battle while Brock, Misty and the other clones along with the bug Pokémon keep Team Rocket occupied.

Mewtwo asks Ash why he's helping him, to which Ash replies that you don't need a reason to help someone in trouble. Mewtwo reflects that Ash may be one-of-a-kind, but Ash says that everyone is. As they reach the heart of the mountain, Ash throws Mewtwo into a healing spring that restores his power, prompting Mewtwo to finally accept that he is a real Pokémon, as the water affects him just as it affected others. The Pokémon clone rises and uses all his psychic powers to move the lake and the spring underground, and then uses his mind-erasing powers to clear Giovanni's mind of Mewtwo, the clones, and Mt. Quena. Team Rocket are transported away from the mountain, with the exception of Jessie, James and Meowth, who had hidden in a cave during the battle.

Ash, Meowth and various Pokémon convince Mewtwo not to erase their minds as well, because though Mewtwo would mean well to do so to keep knowledge of this natural sanctuary hidden from the destructive tendencies of humanity, Ash assures that he would permanently keep the mountain's secret unrevealed at any rate. Mewtwo agrees and personally thanks Ash for all his help and understanding, and he departs on his own as all the Clone Pokémon leave to lead life as natural Pokémon in the wild, sending Ash and co. in a Pikachu balloon and Jessie, James and Meowth in their normal balloon. As Ash, Misty and Brock were walking through a city, Ash hears Mewtwo's voice "I will remember you always". The narrator concludes the movie with the rumors of a Pokémon who traversed the city at night.