It has been a year since Link's visit to Hyrule Castle and the unexpected development that changed his life forever. Now a Hyrulean knight and Princess Zelda's personal guard, Link is tasked with finding the Oracle of Ages, Nayru. Accompanying him on his journey to the town of Labrynna is the princess' strong handmaid, Impa.

However, Link and Impa are unaware that their old enemies, the Twinrova, have returned with Veran, the evil Sorceress of Shadows. Veran manages to trick Link into revealing Nayru's location, allowing her to possess the Oracle of Ages and travel to the past. As Nayru's Harp of Time is the only thing left behind, Link uses it to travel through time in order to stop Veran, aided by Nayru's childhood friend Ralph and a surprising new ally.