Most of the fanbase is most familiar with the Pokemon anime’s interpretation of Mewtwo’s story. The 150th Pokemon was the antagonist in the very first Pokemon Movie, Mewtwo Strikes Back. At the beginning of the Movie, we see Mewtwo gaining consciousnesses behind a glass tube. Dr. Fuji, the head scientist of the cloning project responsible for Mewtwo’s creation, explains to the Pokemon that it is a cloned specimen of a long extinct Mew. Quickly putting two and two together, Mewtwo realizes that it is no more than an experiment to its creators and destroys the lab, including everything and everyone in it.
A deleted scene in the English version that was not released until the direct to video sequel, Mewtwo Returns, depicts a younger Mewtwo, who at this point possesses far more Mew-like features than its mature self. The deleted scene also reveals the motives behind the cloning project and answers the question of exactly why Mr. Fuji agreed to Team Rocket’s project. It turns out that Mr. Fuji is attempting to clone his deceased daughter. Because of the psychic powers Mewtwo wields, it is able to communicate with the scientist’s daughter, as well as several other cloning experiments. Sadly, none of the other experiments are as stable as Mewtwo, and one by one, they die. It adds a darker tone to the movie’s opening, strengthens Mewtwo’s character, and helps explain its struggle with being a clone, as well as its desire to fill the world with similar beings.
However, things play out differently in the canon of the games. In the Lab on Cinnabar Island, where Mewtwo was cloned, journal entries document progress on Mewtwo’s creation. They don’t hint that Team Rocket had anything to do with it. There are also references to Dr. Fuji in the games, who is presumed to be the author of the journal entries.
Diary: July 5
A new POKéMON was
in the jungle.
Diary: July 10
We christened the
Diary: Feb. 6
MEW gave birth.
We named the
Diary; Sept. 1
MEWTWO is far too
We have failed to
curb its vicious
The kind old man from Lavender Town, Mr. Fuji, shares the scientist’s name. Spending his retirement in the small town, he is known to be very good friends with Blaine, the Cinnabar Island gym leader, and is rumored to be the infamous Dr. Fuji, who headed the cloning project. In the generation III remakes, a question mark was included when inspecting a portrait in the lab, suggesting your character recognizes the portrait as Mr. Fuji.
A photo of the LAB’s founder…
In Mewtwo strikes back, the scientists find a Mew fossil, using that to create Mewtwo. In the game, however, the scientists obtain one of the last surviving Mews from Guyana, South America (or at least a fictional representation of the area). There is reason to believe that Faraway Island, an event area where you can obtain a Mew in Hoenn and Guyana, are one in the same. There is a sign on the island that reads:
The writing is fading as if it was
written a long time ago…
“…ber, 6th day
If any human…sets foot here…
again…et it be a kindhearted pers…
…ith that hope, I depar…”
In the Japanese version, it is, at least in part, signed “…ji”; if the entire text were viewable, it could hypothetically say Dr. Fuji. Considering the journal entry was created on September 1st, referencing a losing battle to tame Mewtwo, it wouldn’t be too big of a leap to assume that Mewtwo broke out of the research facility between the 1st and 6th and, remorseful of his actions, Dr. Fuji returned to the island to leave a warning for anyone who would dare go looking for Mew with ill intentions.
A Pokémon whose genetic code was repeatedly recombined for research. It turned vicious as a result.
Mewtwo’s various Pokedex entries suggest that not only was Mewtwo genetically engineered, but was experimented on for many years prior to its escape from the lab. In fact, it is possible that Mewtwo in its original form was not much different from Mew, but the years of experimentation on its DNA continued to morph it into a completely different species.