^ I like that idea. Midna helps him get to the Pedestal of Time and remove the master sword so that Ganondorf can escape. That could be why Midna helps you out from the start. I'm sure I heard somewhere that Midna only helps Link out for her own wellbeing. Maybe she doesn't know how evil Ganondorf is and when he returns Link is just like, "Hey, how's things". Then BANG, he is your next enemy.
Zelda is helping you out and she says "You can only defeat the Twilight King with the Master Sword but by taking it you will release an even greater evil. Then she's kidnapped, you get the master sword, kick the King's ass but... oh no, in comes Ganny.