Kakariko Village:
After the Water Temple, return to Kakariko Village. You'll witness a cutscene involving Sheik and Bongo Bongo. Play Nocturne of Shadow (learned from Sheik) to warp to the entrance of the Shadow Temple.
Shadow Temple:
This dungeon is dark and filled with illusions and invisible enemies. You'll need the Lens of Truth (from the Bottom of the Well as Child Link) to see hidden paths and enemies. Obtain the Hover Boots. The boss is Bongo Bongo. Use the Hover Boots to cross the gap, then hit his hands with the Bow or Hookshot, and attack his eye when he's stunned. After defeating him, Impa awakens as the Sage of Shadow, granting you the Shadow Medallion.