Go to Zora's Domain, watch the cutscene, and go back to Kakariko Village. Once you're there, go find the Shady Guy in front of the wall that Sahasrahla's house is on. If you get close to him, he'll run away, so instead, sneak up on him by merging into the wall. Once you bump into him, he'll tell you the item he stole is at the merchant's shop, and he'll give you the Pegasus Boots.