Mewtwo's Origin

Dr. Fuji and Mew from Ono's manga

As the production of the first ever Pokémon film drew toward a close, the creators turned to the idea of some sort of promotional tie-in. The movie that would be soon playing in Japanese theaters told the story of the cloned Pokémon, Mewtwo, beginning with the creature gaining consciousness, shattering the glass tube in which he had developed, and facing Dr. Fuji and the other scientists that had given birth to him. But what happened before? Where was Mew's DNA obtained? Why did Dr. Fuji agree to create such a powerful monster for the Team Rocket boss, Giovanni? What happened during Mewtwo's development that led to him turning so vicious?

In April 1998, Toshihiro Ono was commissioned to create a tie-in manga about Mewtwo's Birth, given some advance information about the film from which to draw inspiration. His manga was released a few weeks before Mewtwo Strikes Back began playing in Japanese theaters . Ono told one version of the story of Mewtwo's origins, showing Fuji's compassion and friendship with a living Mew, and the eventual creation of Mewtwo, destined to serve as a warrior for Giovanni.

At first I was told to draw Mewtwo's birth, which wasn't included in the movie, so I made a manga out of the first half of the movie (until the part where Ash heads to Mewtwo's island). But after that the anime staff wrote an original Birth of Mewtwo episode that was produced, so there's not much connection between the manga and the movie.
Toshihiro Ono Animerica Interview: Toshihiro Ono
Dr. Fuji, Ai, and Mewtwo from the Drama

At some later point, after asking Ono to make his tie-in, the anime staff decided to create their own version of the story of the Birth of Mewtwo. They took a very different approach from Ono, exploring the past of Team Rocket Organization and creating the character of Dr. Fuji's young daughter, thereby providing a new motivation for the desperate doctor to delve into genetic manipulation. This story was released as an Audio Drama and, in a more condensed form, as a new animated beginning to Mewtwo Strikes Back for home video cassette.

The clones from the animated short

The Japanese home release version of Mewtwo Strikes Back was what was used to make the English dubbed version of the movie, but all but the very beginning of the short was cut for American audiences (although it supposedly remained intact for some international releases).

Due to the rarity of Ono's Japanese Birth of Mewtwo comic, the lack of any release of the Pokémon audio dramas outside of Japan, and the censoring of the animated short in the US, many Mewtwo fans are unaware of even one of the stories of Mewtwo's origin, and so he is often incorrectly labeled as evil. I am glad to be able to share these stories with you, to shed some crucial light on this misunderstood monster's creation and motivations.