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Fairy type Pokemon have "recently" been classified, including well-known Pokemon that previously never exhibited the type advantages of fairy types. The general public accepts the explanation that it was just a matter of inconclusive knowledge about these previously classified mons. However, the evil team this time around isn't evil, just extreme government agents trying to hide the truth while protecting the people by whatever means necessary: the fairies have returned. They appear every 50,000 years to harvest all advanced life in the galaxy. Only you can break the cycle.
The color of you starter determines your ending.