I have too much time to brainstorm

The Calamity was cleansed, Ganon was dead.
Link struggled with his fragmented memories, while Zelda struggled to get caught up to the happenings in Hyrule.
The once mighty kingdom had been brought to its knees and decimated the moment the Calamity struck. It would take much, much, almost too much effort to try and revive a dead kingdom.
Zelda and Link decided to do something that in the past would have probably been considered treason and betrayal- they do not attempt to rebuild Hyrule. The world has prospered in its own way without the interference of a government- why do so now?

Hundreds of years after the Calamity was defeated, a young woman and her husband find long-forgotten papers in their house that had been passed from generation to generation. The words were faint, but a few words could be made out.
"Zelda" And "Link"
"These are nice names," the father commented. The mother glanced to her swollen belly, smiling. "I agree. Have we decided our child's name?"
Meanwhile the current rulers of Hyrule, brought back to defeat a past previous threat, is hunting any and all young blonde-haired, blue- or green-eyed children.
Young Link and Zelda, twins, grow up safe and unknowing of their looming destinies, only preoccupied for finding the origin of their ancient house.

When you have many Links and Zeldas, and one pair finally gets together, you gotta change up their relationship finally for the next pair XD