I like the concept of link losing for once. Okay here goes the Zelda story that I had in my head for a while now:
It starts out with Link and Gannondorf fighting. Link wounds Gannondorf and Links fairy summons the 10 element medallions and shines the beam on Gannondorf, pinning him to the ground. Link tries to preform a fatal blow, but Gannondorf rolls out of the way. Link has his sword stuck in the ground, so Gannondorf take the opportunity to stab Link right through the back.
Meanwhile, on a high passageway above the battle, shadow link watches the original Link get stabbed. The next day shadow link is following behind Gannondorf and his army of Moblins when he realizes that his hand is fading. He concludes that this would be because the original Link was killed and you cant have a shadow without an original object (For shadow link, it was Link because he was Link's shadow).
The whole plot after that is shadow link trying to find all the medallions of the elements from their respective temples. He is also fighting a battle with himself, should he be good, or evil? He finally turns on Gannondorf and defeats him with the recharged medallions. Shortly after the battle he fades away, remembering all the people he saved and helped throughout his adventure.
What do you think?