Ok, we all know that it was stated that Ganon isn't the "main villian" so I have a theory type thing. Maybe the twilight startes to cover the land and the King and the fellow people(and races) blame Ganondorf and the Gerudo's. So they start a war with him and as the game progresses it turns out he's not behind it but some other dark entity. By the end of the game Ganondorf isn't happy about what happend and retaliates, he attacks hyrule and the surrounding areas and you are called to take care of him. But he's still not the final boss.

Sounds good to me, but I came up with it so...

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