In the American dubbed version, the DVD (but not the VHS) features a second mini-feature in addition to the movie feature named The Uncut Story of Mewtwo’s Origin. This 10-minute segment was originally part of Mewtwo Strikes Back’s running length in the Japanese version, but it was cut from the U.S. release of that movie because it was deemed too dark and morose for the film’s American “G” rating. Taken together with Mewtwo Strikes Back, comprise the life story revolving around Mewtwo, one of the more popular Pokémon characters particularly due to his rather human-like personality among most other Pokémon species. They are noted in chronological order below.
A while passes, and a now physical, but young, Mewtwo rests in an unconscious slumber of development inside a containment cell, next to a cell containing the glowing conscience of a cloned Amber. Mewtwo stirs in mind and begins to communicate with the artificial conscience of Ambertwo in a plane of limbo, and the two entities grow a personal bond. This exchange is tragically short-lived, however, as the inability of human science to recreate the human soul catches up with the project, and Ambertwo’s conscious fades into the darkness forever, but she leaves the traumatized Mewtwo with the advice that life is wonderful, and to be alive is the greatest gift he has. Mewtwo, confused by her departure, succumbs to grief and desperately calls out for Amber telepathically, and his brainwaves nearly overload the lab’s systems. Fuji immediately administers a hundred doses of serum, forcing Mewtwo to be subdued into an artificial state of calmness and ignorance of what just transpired. Fuji, emotionally broken by the now permanent loss of his daughter, is now intent on ensuring that Mewtwo, his brainchild, survives.
Alone in the darkness, and unaware of whatever he apparently lost, Mewtwo develops in size and power, tormented in sleep by a single, cryptic question: “Life is wonderful… but why?”
This torment continues until he asks another question to himself: “Where am I?” And with this question he breaks free of his tank but upon learning of the selfish intentions of the scientists and how little they care for him, he destroys the lab and everything in it, which was the beginning of Mewtwo Strikes Back, the first movie.
At the end of the first movie, Mewtwo erased all memory of the events from all those involved. However, due to his not being on New Island at the time, Giovanni has not forgotten about Mewtwo, and has been concocting a military plan of assault upon wherever Mewtwo has settled to take the Pokémon back for himself. He at last locates Mewtwo in his new mountain retreat and begins his operation to assault and capture Mewtwo and bend his will to Giovanni’s. The Team Rocket combat unit heads towards Mt. Quena.
Ash and his friends and Pikachu, on their Pokémon journey as always, are now passing through the area around Mt. Quena, but complications with the weather and the bus service force them to stay at a cabin at the foot of the mountain, where they would meet the Pokémon naturalists Luna Carson and Cullen Calix and the spunky girl Domino from a Pokémon institute. But then a break-in and attempted thievery of Pikachu by the classic antics of the Team Rocket trio Jessie, James, and Meowth, and soon a series of turbulent events involving a scuffle on a hot air balloon, leads everyone into the airspace of Mt. Quena.
There everyone sees the approaching Combat Unit, and Domino, revealing herself in league with Team Rocket Organization as elite Agent 009 (or, as she calls herself, The Black Tulip), pops their balloon and sends everyone else plummeting onto the mountain while she returns to Giovanni to report on Mewtwo’s status. Giovanni’s operation to capture Mewtwo begins in earnest, with Ash and his friends and nemeses caught up in the core of it. Giovanni eventually succeeds in capturing Mewtwo with the threat that the other Pokémon clones would be his to capture and flog if Mewtwo didn’t comply. 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 pokemon that attempted to protect Mewtwo are then locked away in a prison cell. Along with two mother pokemon attempting to protect their offspring. While in the cell Meowth translates what the other pokemon 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.
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 tries 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 pokemon 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.
Ash, Meowth and various pokemon 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. The Narrator concludes the movie with the rumours of a Pokemon who traversed the city at night.