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, while Luna and Cullen go to the spring.
The scene switches over to Mewtwo, who is still in almost unbearable pain within the machines' abilities. He is awakened when he hears Pikachu. Mewtwo is glad his clones are safe, but he also says he can't tolerate the torture for much longer. Ash explains he knew Mewtwo because of Meowth telling him and asks if there is any way to help him. With enormous difficulty, Mewtwo turns and tells them to stop the machines producing the light that is destroying him. Ash and Brock then try to save him by tackling the machines, but that fails as the machine focuses its lens to continue producing black electricity. Mewtwo has no choice but to use the remainings of his power to free himself, risking death if not successful. In a commanding tone, he says either the machines will be destroyed or he will be. Mewtwo turns red, becomes distorted, eyes white, and mouth yelling out all the agony he was going through. But the machines have taken much of his power away from him, as his tremendous effort seems to have no effect. Seeing this, Ash orders both Pikachu to use Thunderbolt on one of the machines. With their combined efforts, the machine explodes, finally releasing a limp and mortally wounded Mewtwo. He falls to the ground with a great thud, with marks, scratches, and bruises all over his destroyed body. Lacking the strength to stand, Mewtwo says weakly that nothing can be done to save him now, as the cost of him destroying the machines was to destroy himself. But when Ash and company try to aid him, Giovanni steps out, making Misty and Brock use their Pokemon to distract Team Rocket. Ash uses this time to carry the broken Mewtwo toward the healing spring with the Best Water Ever.
Mewtwo asks Ash why he's helping him, to which Ash replies Mewtwo saved his Pikachu earlier. Mewtwo asks if only one is enough, and Ash replies that you don't always need a reason to help someone in trouble. Mewtwo reflects that Ash may be one-of-a-kind, but Ash says that everyone is. And as they approach, Mewtwo tells Ash he doesn't know what he is, and soon, it may not matter. As they reach the heart of the mountain, Ash ignores Cullen and throws the pained 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. Giovanni's copter suddenly appears, firing explosives. 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 freeing him from Giovanni's machines. 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.
In the original airing, this was edited to remove the indication of being a three part mid-series special. All DVD releases, including the dub, however, treat it as a film feature special somewhere longer than an hour, rather than a three part special, with it cut on the original airings in the Japanese version due to all three parts airing on the same day. As far as the dub is concerned, there is no theme song for the opening, unlike the Japanese version which contained normal opening and ending theme songs.