The world of Pokémon is a mysterious place, with gameplay mechanics, the animé, and even the pokédex entries becoming the source of weird mysteries. The most fanatic constantly attempt to solve such mysteries, and that resulted in countless theories and straight-up creepypastas. Here are a few questions that captured my imagination, and the best explanations I could come up with.
The Mystery: In the new timeline where Mega Evolution is possible (started by X/Y), a number of Pokémon can transform into temporary powered-up forms with the aid of held items called Mega Stones. These were not created by humans. So how come an artificial Pokémon like Mewtwo has not one, but two Mega forms? If anyone should have a Mega Evolution, it's Mew, because he is the original one, while Mewtwo is only a modified clone. (Also, it would have been a cool easter egg if Mewtwo's Mega Stones also worked on Mew.)
The Theory: In this new timeline, Mewtwo was created by paranoid scientists to protect mankind from the two most powerful known Pokémon in existence, Mega Rayquaza and Arceus, should either of them ever turn against humanity. So they took Mew's DNA and used it to make the ultimate Pokémon. The result was indeed very strong, but still not strong enough to counter those powerhouses. So the scientists started researching Mega Stones and Infinity Energy, until they finally managed to artificially produce two special Mega Stones to aid Mewtwo in such a hypothetical battle.
Mewtwonite Y greatly boosts Mewtwo's Special Attack, and increases its base stat total to 780. Mega Rayquaza's base stat total is... also 780. Coincidence? This, along with Mewtwo being capable of learning powerful Ice-type attacks such as Ice Beam and Blizzard, would make the Genetic Pokémon humanity's best bet against Mega Rayquaza, should the legendary dragon ever go on a rampage (even with Delta Stream lowering the damage of those moves). Mewtwonite X, on the other hand, not only greatly increases Mewtwo's Attack, but also adds a Fighting sub-type. While Arceus can change his type with its plates, its original type is Normal. Thus, Mega Mewtwo X would not only have a higher base stat total than God, it would also have a type advantage to it.
The Mysteries: The Nido line was the first in Pokémon history to have gender differences (even before genders were introduced, in fact!). Despite that, an interesting glitch has been plaguing the family since Generation II. Basically, Nidorina and Nidoqueen are not recognized by the games as the female versions of Nidorino and Nidoking. They are both in the Undiscovered Egg Group, which means they can't breed, not even with Ditto. This results in the somewhat creepy scenario when Nidoking can mate with a Nidoran(F), but not with a Nidorina or Nidoqueen. More like Pedoking, amirite?
Also, it's worth mentoning that Shiny Nidoqueen is the source of another mystery. In the first two evolutionary stages, Nidos of both genders take each other's regular color schemes when Shiny. In the final stage, however, Shiny Nidoking goes blue (which is the color of regular Nidoqueen), but Shiny Nidoqueen goes green. Regular Nidoking is purple, so Shiny Nidoqueen commits a serious dress code violation with that move. Why am I talking about these two things at the same time? Because, perhaps, these two mysteries are related.
The Theory: The female Nido's life cycle is the story of a confused girl realizing and accepting the fact that she's a lesbian. Sounds weird, I know. Bear with me. As a Nidoran(F), she desperately tries to fulfill the traditional female role of supporting her man and eventually becoming a mother. As such, she's willing to try for baby, while her Shiny form goes along with the reverse color scheme thing, agreeing they'd look cute together that way with Shiny Nidoran(M). When she evolves into Nidorina, she starts doubting herself, realizing she isn't happy. As such, she starts turning down Nidorino's advances in private. She also turns a blind eye to Nidorino seeing Ditto, accepting that he has urges she no longer wishes to satisfy. The Shiny form still goes along with the reverse color scheme thing to make sure the family and friends don't suspect anything is wrong, not wanting to embarrass Shiny Nidorino. By the time she evolves into Nidoqueen, she goes through a lot of soul searching, finally deciding this relationship will never work out. Thinking all man are pigs and she's better off without them, Nidoqueen becomes a strong, independent feminist, and her Shiny form turns green out of spite. Shiny Nidoking keeps up the reverse color in memory of her, while struggling to accept that the only way to produce Nidoran offspring is with either Ditto or underage girls. He goes to Ditto with tears in his eyes.