A few years after the battle with the Calamity, Hyrule continues its restoration with the aid of the surviving royal family; when an mysterious fog arises underground, Link, Kate, and Zelda go in to investigate, only to find and awaken the real Ganondorf; Ganondorf's attack sends Zelda away, a Master Sword breaks, Link loses his arm, and Hyrule Castle begins floating skyward; Link, Kate, and Sheik must travel around Hyrule once more, even going skyward to find and save Zelda before it's too late.
as an evil darkness threatens their home, 11 year old's Link and Kate embark on a quest to seek help from Princess Zelda, leading them onto a bigger quest, and even through time, to stop the darkness, Link and Kate must recover the three spiritual stones and awaken the sages before they are slain by the very darkness that threatens them.