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You all have to learn to separate this information
First off, we all now know that Kanto "male" Mewtwo and Kalos "Female"Mewtwo are 2 different Pokemon. With the statement that the Pokemon company issued, this is applied to ALL Pokemon mediums
The anime will explain it in its own way
The games will explain it in its own way
The manga will explain it in its own way
People often make the mistake of mixing canons when they forget they merely share coincidences yet diverge into separate matters
The issue that's stopping any of us making consistent theories is Team flares motive and structure of operations. Without knowing that, we are just guessing out of our asses
Ever since the major update to how story is told in black and white, anything can fucking happen; since we haven't seen story play a strong role in this since ever.
Kalos Mewtwo may have been created by Team Plasma/or an operative from there like colress
Or by Team Flare
Or an ex-TR member, or someone else entirely
All we know is that there are 2 mewtwos. For us to speculate correctly, we all need to file our ideas and make them consistent with one another and contrast them from others that contradict it and belong in a separate bubble
But /vp/ is too lazy for that