Changing my idea for the villain. He is no longer the same Ganondorf from OoT.
Ok, then instead of my part of the story where Ganondorf comes out of the portal, take the portal out completely. The men who attack the church (Ganondorf's Dark Disciples) steal one of the six medallions from the church (maybe the light or the forest one). Link follows the Disciples back to a secret meeting with Ganondorf. He finds out that the ambassador from the Gerudo nation is planning to uncover the secrets of the Triforce. At this point in time, most people think that the Triforce is an ancient and mythical item that doesn't exist. Ganondorf finds Link spying on his meeting and sends his Disciples (all six of them, one holding one of the medallions) after him. After he collects all of the medallions, Link is lead into Old Hyrule, the abandoned under city that hides the ancient temples that the Hero of Time traveled through years earlier. Someplace down there he runs into Ganondorf.
I have no idea what I am going to do from there, but that is what I have so far...