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Anyway, if I'd have to chose the "darkest" game maybe it could be BW2 where Ghetsis literally (in the JP version) says "I will kill you!" or Lysandre wanting to destroy everything with that weapon. Then again, no pokémon game has a dark setting.
Maybe, and only maybe, the only pokémon with a dark setting could be Mystery dungeon since everyone treats you like scum after they find out you're a human.