In my story Ganondorf has learned not to underestimate his opponents. He is using his power and some of his allies to pull the Triforce out of possessing the Hero of Courage.
At a critical moment near the final of the game, Shiek must decide whether she will reveal whom she is and use her true power. It would be during a boss battle, and the entire party will be dead but her, and you will for the first time get to use a new magic attack that will totally kick ass...however, once that is unleashed Ganondorf will know who the Sage is and act 2 of the story will began to hunt her down.
At this point in time, he already has the triforce of courage. So basically, you wouldn't have to bring Link into the game at all.
The ending of this story wouldn't be a traditional happy ending, because Ganondorf must win. However, in the last battle it is the Sages that sink Hyrule underwater and protect it from Ganondorf's evil. In this way, the world doesn't have to turn dark.
With Ganondorf free in this new world, the uncertainty of the legend becames a reality even for him. Will there ever be another Hero of Courage after he pulled it out of the past Link? How about another Zelda with the triforce of courage? He rules the islands of Wind Waker, yet he doesn't rule the world he loves.