Zelda: Winds of a New Beginning

Zelda: Winds of a New Beginning/Darkness are fanfics by Alaia Skyhawk.

New Beginning follows Link four years after the events of Wind Waker and Phantom Hourglass. It is 89 chpaters long.

New Darkness follows Arkai as he passes trials to become a Hero. It is ongoing and currently at 48 chapters.

They can be found here and here.