After completing the Water Temple and obtaining the Lens of Truth from the Bottom of the Well, Link will encounter Sheik in Kakariko Village. Sheik tells him about an evil spirit and will teach Link the Nocturne of Shadow allowing him to enter the Shadow Temple. The item to obtain in the dungeon is the Hover Boots. The mini-boss is a Dead Hand and the boss of the dungeon is Bongo Bongo. After he's defeated Impa, Princess Zelda's nursemaid is awakened as the Sage of Shadow.
The Shadow Temple has 4 floors and is infested with quite a few Redeads. Along the walls there are many paintings which give out clues, that only Navi can hear. There are alot of fake floors and walls which can be seen if the Lens of Truth are being used. Near the boss chamber there is a large gap which can be crossed by using the big ferry, which will only move after playing Zelda's Lullaby. Once the ferry almost reaches the other end of the gap it will sink, taking Link with it if he doesn't jump off quickly.
- The ferry that Link takes to the boss room is a reference to Charon, the ferryman who carried the dead across the river Styx in Greek mythology.