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In Pokémon Red and Blue, and the remakes Fire Red and Leaf Green, the journals found in the ruined Pokémon Mansion refer to Mew giving birth to Mewtwo:

Diary: Feb. 6
MEW gave birth.
We named the newborn MEWTWO.

Bulbapedia further states that Mew was already pregnant with Mewtwo when it was encountered, though it offers no source. If we take this at face value, though, Mewtwo is Mew's biological offspring, and was turned into its present form through "years of horrific gene splicing and DNA engineering experiments".

However, there appears to be some debate, both here on SE and elsewhere, about whether this should be taken literally, or whether Mewtwo's creation was purely artificial and the "birth" referred to in the journal is only figurative. Interestingly, while the Japanese version of Let's Go! Pikachu and Eevee still refers to Mew giving birth, the English translation does not.

In the anime, it's known that Mewtwo was cloned from Mew's DNA, so I'm asking specifically about the version of Mewtwo in the games. Was it conceived and born naturally, or was it created from scratch? Is there any conclusive evidence other than the diary entry?

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    a good source might be to look at the japanese versions of the red/blue fire red/leaf green. It could be a translation error on the games part. – Himarm Feb 10 '20 at 7:55

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