Arriving in Symmetry City in the present, Link finds that it has been ruined. He travels to the past and learns that the Tuni Nut that maintains balance in the village has been broken. Traveling south to Restoration Wall, Link finds Patch, the Restoration Guru. By completing Patch's Restoration Ceremony, the Tuni Nut is restored, and Link returns it to its rightful place. Link returns to the future, in which the town is no longer ruined, and finds that a doorway has appeared in what was earlier a volcano. He then enters the doorway and finds himself in the Skull Dungeon.
The Skull Dungeon is named for the shape its map takes; in this case, the map takes the shape of a skull. The dungeon has grey floors and green walls. There is magma found throughout the dungeon; this makes sense, considering that the dungeon is inside a dormant volcano. A new kind of puzzle is introduced in this dungeon; in two of the rooms, all of the floor tiles are blue. Link must turn all of them red by walking over them, while navigating around Armos Statues that block his way and without backtracking. Solving the first one of these rooms earns him the Switch Hook, and the second gives him a Small Key. Mine Carts can be found throughout the dungeon.