I've been thinking a lot about the Wind Waker lately and I have a theory.
Before Hyrule is flooded by the goddessess, Ganon rises again, yet he goes unchallenged. Out of all the times he's come back, this is the only known time where he's risen and there's been no Link to save the world.
My theory is this: there was a Link that was meant to stop him. However, instead of failing to do so (which would've made him the weakest of all the Link's) he's corrupted instead. Either via torture or threats to those he cares about, he joins Ganon and becaomes evil: the first and only true dark Link. Of course, with Link by his side there's no one powerful enough to resist him (as almost all the games have shown, Link is frequently the only one that even tries).
Link was then also used much like Vader was used by Palpatine. He's sent off to kill all the surviving sages (presumably the ones shown as ghosts in The Wind Waker) and then Zelda. Presumably Link also did something about both the leaders of the other races (I've the image of him having a Ralis-like Zora as his pet) and the other spiritual beings.
With the destined hero evil and everyone else that stood a chance against him dead, the gods did the one thing they could do: flood the world and wait for the next Link.
It would explain why the Master Sword wouldn't be at full strength (tainted by dark Link) and why Ganon was finally deemed a threat enough for the gods to intervene.
Anyway, that's enough of that, I'm finishing the fic now cause I lost my inspiration but now it's back (apparently it only works in the am's).
How come 75% of the fic posted at mychemicalslash lately seem to have Frankie in the pairing, yet hardly any have Bob?