After the liberation of the seven maidens and the final defeat of Ganon, Link and Zelda lived in peace for the rest of their lives.
..... To restore order in the land, the three goddesses of the tri-force decided to take the lands of the defeated enemies and rule them: Farore would take control of the Armos Knights Castle; Din would rule the Lanmolas Desert; and Nayru would watch through the windows of Moldorm's Tower.
..... They lived and had descendants in their new kingdoms, but their successors were corrupt by the remainder power of the Dark World and became evil. They entered into a long war that took the lives of hundred of citizens.