My theory is this: Hyrule's had peace for X amount of years since Ganon got sealed away in OoT. So since everybody's let their guard down, a new evil has taken over. Link can't defeat it, so he needs help from the one guy he'd never want help from in Ganon, as he would know the most about controlling evil. So Link releases Ganon from the Sacred Realm. Ganon doesn't want to help Link, but sees this as a territory thing, and doesn't want somebody else trying to steal his glory. Of course, this'll only work until Ganon and Link beat the evil and Ganon tries to take over the world himself.

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Thanks to Tracheon Black for the sig and Sakaki-chan for the avatar!
My BA character
My Zelda fanfic/ All the TP trailers!
"Rabid Wolverine" Chris Benoit. 1967-2007. We will all miss you, Chris.