You probably think you know how Mewtwo came to be. Most people do. You’ve seen the 1998 movie, or maybe you read the brief, scattered journals left behind in the scorched remains of the Pokémon Mansion on Cinnabar Island. Scientists found Mew, they played God, and they created a monster. It’s a classic sci-fi trope wrapped in a Nintendo-approved package. But that’s the sanitized version. The reality? The uncut story of Mewtwo’s origin isn’t just about a clone gone wrong. It’s a tragic, unsettling narrative involving human cloning, a dying child, and a psychic trauma so deep it basically explains why Mewtwo wanted to erase humanity in the first place.
If you grew up in the West, you missed the most important part of the story.
When Mewtwo Strikes Back hit theaters in the United States, Warner Bros. and The Pokémon Company made a choice. They lopped off the first ten minutes of the film. They figured kids couldn’t handle the existential dread of a philosophical debate between a group of baby clones. Honestly, they were probably right, but it left a massive hole in the lore. To truly understand this Pokémon, you have to look at the The Birth of Mewtwo (Mewtwo no Tanjō), a radio drama and animated short that gives us the gritty, uncensored details.
Dr. Fuji’s Real Motivation Wasn’t Power
In the version we got, Dr. Fuji is just another generic mad scientist working for Giovanni. He wants to create the world’s strongest Pokémon because, well, that’s what villains do. But the uncut story of Mewtwo’s origin reveals a much more desperate, human motivation.
Fuji wasn’t obsessed with Mew because he wanted a weapon for Team Rocket. He was obsessed with cloning because his daughter, Amber, had died in a tragic car accident.
He was a grieving father using Team Rocket’s funding to bankroll his own private resurrection project. He wasn't just cloning Mew; he was trying to clone Amber. He had her consciousness—or at least a digital representation of her memories—stored in a vat. In the secret laboratory on New Island, Mewtwo wasn't alone. He grew up in a psychic link with three other clones: Bulbasaurtwo, Charmandertwo, and Squirtletwo, along with the "copy" of the doctor's daughter, known as Ambertwo.
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They communicated telepathically while their bodies developed in those glowing green tubes. It was a weird, underwater dream world. Ambertwo taught Mewtwo about the world, about the sun, and about what it meant to be alive. She was his first friend. She was his only friend. And then, because this is a story about the fragility of life, the clones started to fail.
Why Mewtwo is Actually Traumatized
One by one, the life lights of the starter clones flickered out. They weren't stable. Then, Ambertwo began to fade. In the uncut footage, we see their psychic forms dissolving into white light. Mewtwo, still a child in this mental landscape, panics. He doesn't understand death yet. Ambertwo’s final words to him are devastatingly simple: "Life is wonderful."
Then she disappears.
The scientists monitoring the vats watch Mewtwo’s brain waves spike. He’s experiencing a level of psychic distress that would literally kill a human. To save their "investment," Fuji and his team do something arguably worse than the cloning itself: they forcibly wipe his memory. They use a chemical sedative to erase the existence of Ambertwo from his mind so his powers don't spiral out of control and destroy the lab.
So, when Mewtwo finally wakes up and destroys the scientists in the movie’s opening scene, he isn't just a "jerk." He’s a creature who has been subconsciously mourning a loss he isn't allowed to remember. He feels an empty void where his first social connections used to be. That’s the core of the uncut story of Mewtwo’s origin. His hatred for humanity isn't just "I'm a clone and I'm mad about it." It's a deep-seated, biological reaction to being used as a lab rat by a man who was trying to replace a dead daughter.
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The Cinnabar Island Journals vs. The Anime
Video game fans usually point to the Red/Blue/Yellow journals as the definitive source. They’re great for atmosphere. "Mew gave birth," one says. That line alone caused decades of confusion. Did Mew literally give birth? The Japanese text is slightly more ambiguous, leaning toward the idea that they "found" a newborn Mew or implanted the embryo into a Mew.
But the uncut story of Mewtwo’s origin in the anime is what actually gives the character a soul. In the games, Mewtwo is basically a legendary encounter—a boss at the end of a dungeon. In the uncut lore, he’s a victim of the "unnatural."
Think about the ethics here. Dr. Fuji was funded by Giovanni, the leader of a criminal syndicate. This isn't just a "science gone wrong" story; it's a "military-industrial complex exploiting grief" story. The reason Mewtwo is so obsessed with the "purity" of clones versus "natural" born Pokémon in the movie is that his entire existence began with the failure of natural life. He was born from the ashes of a family tragedy.
The Difference Between the Japanese and English Dubs
It’s not just the deleted scenes that change the story. The script itself was butchered. In the original Japanese version of the film, Mewtwo’s dialogue is much more philosophical. He isn't trying to take over the world like a cartoon villain. He’s asking: "Who am I? Why am I here? Who asked for me to be created?"
The English dub turned him into a guy who wants to rule the world with an army of clones. It’s a huge disservice to the character's complexity. By removing the uncut story of Mewtwo’s origin involving Ambertwo, the localization team stripped away his humanity. They made him a monster so it would be easier for the "good guys" to beat him.
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If you watch the uncut version, Mewtwo’s eventual decision to leave and find a place for his clones isn't just a surrender. It’s a realization that he can't find the answers he's looking for by fighting. He’s still that lonely kid in the tube, looking for the light Ambertwo told him about.
Why This Matters for Fans Today
Understanding the uncut story of Mewtwo’s origin changes how you play the games. It changes how you look at Mega Mewtwo X and Y. It makes the "Mewtwo Returns" special—where he’s just trying to live in peace on a mountain—actually make sense.
He’s the only Pokémon with a backstory that rivals a Greek tragedy.
If you want to experience this yourself, don't just take my word for it. Go find the "The Birth of Mewtwo" prologue. It’s available on various archival sites and was eventually released on some DVD versions as a bonus feature. It’s only about ten minutes long, but it will completely reframe your childhood.
Actionable Steps for Lore Seekers
- Watch the "Uncut" Prologue: Search for "The Birth of Mewtwo" or "Mewtwo’s Origin" on video platforms. It’s the 10-minute segment featuring Ambertwo.
- Compare the Scripts: Look up the side-by-side translation of the Japanese "Mewtwo Strikes Back" vs. the English dub. The philosophical differences are eye-opening.
- Re-read the Cinnabar Journals: Go back to the Pokémon Mansion in FireRed or Let’s Go Pikachu. Knowing about Dr. Fuji’s daughter makes those clinical notes feel much more sinister.
- Check out the Radio Drama: If you can find a translation of the Mewtwo no Tanjō radio drama, it goes even deeper into Fuji’s descent into madness and the expedition to find Mew’s DNA in the jungle.
The story of Mewtwo is a reminder that even in a franchise built for kids, there are layers of storytelling that deal with some pretty heavy themes: grief, the ethics of cloning, and the search for identity in a world that sees you as a tool. Mewtwo isn't the villain of his story. He’s just the only one who survived the experiment.