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Mewtwonite is actually the Mega Stone of an extinct Pokemon that was a closer descendant of Mew
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My god... how did we not see this before... not Mewthree, but rather... Mewpointfive.
Although, something you said earlier did make me think, huh, you know, Pokémon as a whole seem remarkably immune to that whole (actual) evolution thing... I mean, the Fossil Pokémon died out, sure, but other than that, Mew is just about the only evidence we have that says that Pokémon species either adapt or die out over time. And the fact that some Mew still exist show that individuals of the older species must have long lifespans like whoa... but that could be. Mew obviously has a lot of descendants, so I wouldn't be surprised if some of them got lost in the mix.
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alternative idea
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Also possible, and it would explain the presence of multiple Mewtwonite in XY and ORAS, but at that point, aren't we essentially saying the same thing as "The Stones made by the weapon just happened to align with an artificial Pokémon that hadn't been created yet, out of sheer coincidence?" Or maybe I'm misunderstanding the idea here.