This is similar to the RPG I'm doing at
my forums. Wumpi Chan and I thought it all up.
I would make it like 5,000 years after OOT, with some small changes to the same Hyrule. An evil member of the royal family does some major crime or something, and he is banned from Hyrule to the desert. There he meets a highly skilled desert tribe, and maybe 5 years later he gains full respect from the tribe, and he decides to get his revenge on the royal family, so they assassinate every member of the royal family. So there is no royal family, so the Triforce goes all corrupt-like because the royal family holds it together or something. Like the Triforce used to resist evil, but now it accepts it, so basically, the evil dude gets the Triforce, and kills the tribe and says they killed the royal family. The Hylians beleive him and makes him King because of his previous ties to the family. Then like a week later he senses like the only power between him and conquering the world; Ganon (who is in his Ganondorf form all the time, but full Ganon power, because a monster just wouldnt look right in this game), who just came back to life, or whatever, and he's fighting Link's ancestor, who is like really skilled too. They both fight for a while and they're really tired and everything, so the evil dude arrests them both with ease, with a soon execution date. While in prison, Link and Ganon form an alliance, sort of like how Piccolo and Goku formed an alliance at the very beginning of DragonBallZ, but of course, Ganon stays evil at the end. So they break out of the prison and soon learn that the goddesses are become corrupt aswell, because of the evil in the Triforce. So Link and Ganon go on a quest to each goddesses' shrine to... uncorrupt them, I guess, by facing trials and stuff. They do the first 2 alright, and then on the third they do the trials but as soon as they get to speak with that goddess, she goes evil. She's about to kill everything when the other two goddesses show up and hold her back. They tell Link and Ganon to find the one surviving heir (who is like a little kid) to the throne, and take him to the castle. So, they do so (not easily, of course, they have to do alot of crap to find him) and go to the castle to destroy the evil dude once and for all (who is really strong because he has all of the Corrupt Triforce's power). So they fight and in the end the heir helps somehow, giving them some kind of magic power or something. So they win, and a few weeks later the heir is on the throne again, and Ganon bids his farewell to Link, saying they still had a score to settle one day, though. Link says he is looking forward to it, Ganon leaves Hyrule, and Link gets some sort of cool position in the Hyrule Castle. I was thinking maybe the heir was Link's long lost brother or something, and Link becomes his bodyguard to watch over him, and the heir doesn't remember him or something but that really doesn't fit...