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If M16: Pokémon: Genesect and the Legend Awakened used the M01 Mewtwo as originally planned.

The Holy Cat

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If the the movie crew used the M01 Mewtwo instead of creating a new Mewtwo character due to that character being owned by the Takashi Shudo estate, would they probably retcon that faraway city from the ending of Mewtwo Returns to be in Unova? If they did that retcon, it would probably had connected Ash and Mewtwo's character journeys, especially since Ash, Ash's Pokémon including his Pikachu, Misty, Brock, and the Team Rocket Trio were allowed to keep their memories of their second encounter with Mewtwo at the ending of the special.
 
If I had to come up with a way for there to be a second Mewtwo, it would be to use a continuity error from way back in Indigo. Namely, that Bill knew what Mewtwo was enough to have an image of it engraved on his door.

And Bill, as we know from the games, would do anything for rare pokemon...

So I'd handwave a little story about "a researcher from Johto, lives in a lighthouse" had left the project before completion, thus being able to survive the devastation of New Island, but his curiosity got the best of him so he took what research he had and decided to study the finished product...which involved finishing the project with his own data.
 
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