At some point she died, though he wouldn't emerge from his prisons until eons afterward. The hero died, his princess died. Hyrule decayed, but the goddesses had blessed their beloved land, and though it came close to waning to an empty tomb, the city always rebounded. He and the city flowed like the tides, bound eternally to rise and fall.
There were hints of his memories trapped in Hyrule still; though Link, accursed boy, was buried and his past a myth, here Ganondorf could see a tunic of green, and here the best mare of the herd was Epona. The first born princess always received Zelda's name, even when she unfit to bear it. Here someone carved a triforce into the rock to protect his family, and here someone sang the royal lullaby to her child.
And on clear nights, after darkness descended and the rest of Hyrule slept, Malon's voice echoed across the plains.