Fridge pages are Spoilers Off by default, so all entries have been folderized as a security measure. Proceed with caution. You Have Been Warned!
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- Why in the world is this Mewtwo a girl (in theory)? If you have the female with the male that already exists, you can let them mate, kill the parents, and raise the kid as your weapon. Alternatively, for science.
- Where did the second Mewtwo come from? An aversion of No Plans, No Prototype, No Backup - whoever made it, used Team Rocket's data.
- Mewtwo's backstory (and indeed, existence) raises a lot of unanswered questions when one thinks about the details.
- Who is the obviously non-Team-Rocket-affiliated group that created it (and was both rich and technologically capable of doing so), and why did they go to the trouble of creating it?
- Where and how did they find DNA of Mew - a rarely-seen Mythical Pokémon thought to be (nearly) extinct?
- How did they know the exact alterations to make to the DNA to create a Mewtwo physically identical to the original, when no indication is ever given that they already knew about Mewtwo?
- How did they come up with the name "Mewtwo", when no indication is ever given that they already knew about Mewtwo?
- How did they get a second Mewtwo made on seemingly their first go (there's no indication it wasn't), when the original Mewtwo was preceded by many failed attempts? And when no indication is ever given that they already knew about Mewtwo?
- What was the point of electrocuting it once it was created, other than to show that the scientists were bastards (and pretty stupid ones at that)?
- So Ash briefly mistakes Mewtwo for the original, showcasing he still remembers it... and no-one bats an eye at him knowing about the never-before-seen Genetic Pokémon? And he never brings it up again? And Mewtwo never asks how Ash knows about it despite being alive for only a few days? It never even looks into his mind to find out that there's another Mewtwo running around?
- While the exact nature of the Red Genesect's mind control ability is unknown (Psychic Powers or something technological?), one must wonder what went through Team Plasma's head when they decided to not use a version of it to control their superpowered cyborgs themselves, while also giving/retaining the Red Genesect's ability to control the others and ensure a totally disastrous rebellion.
- Unlike in the games, Mega Mewtwo Y seemingly has no drawbacks — it can be activated at will, Mewtwo is able to do it from birth, it bestows enhanced speed without any attributes being weakened, and no mention is made of it being strain-inducing or anything. By all accounts, Mewtwo has no reason to not use it all the time, yet there are several moments where it reverts or otherwise doesn't use it for no apparant reason.