Kakariko Well and Shadow Temple

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After you've beaten the Water Temple, go to Kakariko Village again. There'll be a house there in flames and Sheik will come and tell you about the demons that have come out of the well. Watch the scene for a moment, and when Sheik talks to you again, he'll teach you the Nocturne of Shadow. After that, go to the windmill and talk to him, then show him the ocarina. He'll teach you the Song of Storms, which lets you make the rain on or off at any time anywhere! Now that you know the song, go to the temple of Time and revert back to your younger form, then go back to the windmill. Play the Song of Storms for the man, then leave the windmill and climb into the well.

From the start, go down the hallway and walk right through the wall at the end of the room. You'll go right through and appear in the next room! From there, take the path to the right and as you make the left, walk through the wall around the corner and open the chest to get a key. Continue down the hall and make another left at the end. Stand on the Triforce symbol on the ground and play Zelda's Lullaby to drain all the water in the well. At the end of this room, make a left and go down the hallway while trying to avoid the green flying skull thing. About halfway down the hall turn right and enter the next room. Light all the torches with Din's Fire to open the caskets then look in the one in back and to the left to find a key. Now, get back to the main hallway and continue down to the right. After you turn left again, walk through the wall and open the chest to get a key. After that, jump into the pit and crawl through the opening to reach the next area. Enter the next room and you'll see four arms sticking out of the ground. Let one capture you, then the main enemy will appear. Struggle to get out of the hand's grasp, then as the enemy lowers its head, attack with your sword. Repeat the process until he's defeated to get the Lens of Truth! Now, warp to the Temple of Time and become Adult Link again and play the Nocturne of Shadow to warp to the entrance to the Shadow Temple. From the start, walk up to the pit and use the Longshot to cross the gap to the other side, then walk right through the wall in front of you! In the next room, use the Lens of Truth to point out the real skull on the pedestals. Then, push the bird statue so that its beak is aiming at the real skull to open the door. You can't reach that door yet because a chasm separates you and the door, so turn around and use the Lens of Truth to find two passages in the wall. Enter the one to the right and in the next room, walk through the wall and go right. Use the Lens of Truth to reveal another secret area in the right wall. Enter that room and defeat the zombies and bats to get the Map then go back to the previous room and go right. Use the Lens of Truth to find yet another passage and go through it to reach the next room. In the next area, take the right path and walk to the end of the room and walk through the wall at the corner and open the door to the next room. In this room, you'll see four arms sticking out of the ground. Let one capture you, then the main enemy will appear. Struggle to get out of the hand's grasp, then as the enemy lowers its head, attack with your sword. Repeat the process until he's defeated to get the Hover Boots, which let you walk across water and air for a short period of time! After you get the boots; backtrack to the room with the bird statue and the door across the chasm and strap on your Hover Boots. Run across the chasm and go through the door to the next room. Go down the hill in the next room and defeat the Beamos statue with bombs, and then walk through the wall to the left. Find all the silver rupees to open the gate and get a key from the chest. Go back to the last room and bomb the remaining wall to the left and enter that room using a key. Run all the way to the big, open section of the room while destroying the Skulltulas along the way. Then, jump from platform to platform while avoiding getting cut by the guillotines until you reach the back of the room. Defeat the Stalfos Knight here and go right and wait for the moving platform to reach its lowest point, then jump down onto it! When it gets high enough, jump onto the small ledge to the right and walk along it to the other plateau. Get all the visible silver rupees then bomb the Beamos statue to find the last one to open the door. In the next room, use the Lens of Truth on the wall to the right to find a hidden block. Pull the block out to the center of the room and push it through the room because it protects you from the spikes from above! At the end of the path, get to the other side of the block and climb on top of it, and then jump to the ledge to the right near the jail cell. Push the switch there, and it'll make a chest containing a key appear. Use the Longshot on the chest to cross the gap to reach the key. Now, leave the room and go back to the previous room. Cross the small ledge to the platform halfway across and jump down to the platform with the guillotine. Use the Lens of Truth to reveal the hidden platforms behind the one you're on and jump onto the first one and wait for the moving platform to reach you, then jump on! Ride it to the door and enter the next room using a key. In the next room, use the Longshot and the Hover Boots to collect all the silver rupees, then enter the door that just opened. Climb up the ledges to the top and throw a Bomb Flower into the flames of the moving skull statues. Do that until all three statues are destroyed, then drop down and get a key. Go back to the room you were just in and use the Lens of Truth to reveal all the Longshot targets, spikes, and ledges and aim at the target above the door to the left. Enter that door with a key and put on your Iron Boots and walk past the Blade Traps and going against the fan's wind gusts. Continue until you reach a pit, then use the Longshot on a wooden pole on the ceiling to cross the gap! Then, drop into the second pit in front of you and keep your Iron Boots on so you don't get blown away. When you reach the door, turn around and put on your Hover Boots and use the Lens of Truth to reveal the area behind the wall. Have the fan blow you across the gap to that hidden section and open the door to the next room. In the next room, put a bomb on the garbage pile and then use the Lens of Truth and it'll reveal a chest with a key. Defeat the two mummies there and open the chest to get five rupees, then open the door with a key and enter the next room. In the next room, pull the block along its path until it falls into the small crease in the floor. Then, climb onto the block and jump onto the higher ledge and jump onto the ship nearby. Play Zelda's Lullaby on the Triforce symbol to get the ship moving. Defeat the Stalfos along your journey and when the ship stops at the end, put on your Hover Boots and run towards the dock down below. When you touch the ground, enter the door nearby to the next room and make your way through the maze of invisible walls to the right side of the room and enter the door. In this room, the spiked walls will attempt to crush you in, but just use Din's Fire to destroy the walls and defeat the zombies to reveal the chest with the Boss Key! Leave the room and get across the room to the other side and use the Lens of Truth to reveal the hidden hand enemies. Defeat them and their smaller counterparts to get a key. Now, go back to the room where you landed after the boat ride and stand between the pots at the inner edge of the platform. Shoot an arrow at the Bomb Flowers to detonate them and destroy the base of the statue! Walk across the fallen statue and enter the next room with the key. Use the Lens of Truth and the Hover Boots to cross the hidden platforms to the Boss's Room! To defeat Bongo Bongo, shoot one hand with an arrow or two to freeze it. Do that to the other hand to freeze the other hand to expose the eye, which is the weak spot! Shoot the eye with an arrow and then run in and attack with the sword. Repeat the process to defeat it and to meet Impa again as the Sage! After she gives you the Shadow Medallion, head out to Gerudo Valley!