In the aftermath of TotK, the world is in a sorry state. The sky islands are falling, violent quakes closed the access to the depths, and embers of darkness (fragments of the secret stone last held by Ganondorf) have fallen to the land and created fields of distortion where the present world has been over written by a section of the past. The worst are the dungeons, where the fragments empower new boss monsters.
Link and Zelda team up together to restore Hyrule with the new gameplay gimmick being the ability to swap between them. Link as a swordsman and Zelda with time powers (some inspiration from Bioshock infinite’s Elizabeth).