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The next sage lies in Kakariko Village. Upon entering the town, you will find that it is on fire. Sheik is there, overlooking the village well. Suddenly, the well's pulley system smashes apart! An invisible force comes out of the well and soon turns and tosses Sheik around. It then generates into a purple, formless monster. It runs around the village and then comes for you. You get ready to defend, yet it attacks you and knocks you out cold.
Once you regain consciousness, Sheik will explain the situation to you. An evil that was sealed inside the well has escaped to the Shadow Temple in the Graveyard. Impa (Zelda's former attendant) has gone to the temple to battle it. Sheik then teaches you the melody that will lead you to the temple, the Nocturne of Shadow.
The Nocturne of Shadow:
Before you enter the well, you will need an item that will allow you to see invisible items, enemies and passages, the Lens of Truth. It lies at the bottom of the well. Unfortunately, the well is sealed off, so you will need to return to the past and retrieve the item as a child.
Enter the windmill that is directly in front of the well. The angry music man inside claims that seven years ago, a child with an ocarina played a strange song that messed up the windmill. Pull out your ocarina. The man will remember the song and teach it to you. (It is the same melody playing in the background.)
The Song of Storms:
Head to the Temple of Time and return the Master Sword to it pedestal. Return to Kakariko Village (You can use the Nocturne of Shadow you just learned.) Enter the village windmill and play the Song of Storms. The windmill will drastically speed up, and the water in the well will disappear. You are now free to access the well bottom.
Crawl through the tunnel at the well's entrance. Drop down the cliff and kill the Big skulltula. You will see a skeleton lying against a wall. Walk through that wall. It is not real. The Lens of Truth in this dungeon will allow you to see what is real and what is not. In the next room, stay on the main path to avoid falling into invisible pits. Head for the south west corner of the room beneath the Reservoir.
Go across the pool of water in front of you and into the narrow trench. (It is filled with water.) Go left or right down the trench, and follow it around two corners. (A gigantic Green Bubble is wandering around so be careful.) After the second corner, run halfway down the hall until you reach an area where there is a triforce inscribed on the floor. If you want to get there faster, run through the area where several logs are and go through this second fake wall and you'll end up in another room. Do not go directly through the area where there is a set of hanging log arches on the floor, because there is a pit hidden there. There is also a Wallmaster lurking in the room, so stay alert. Go to the furthest dead-end of the room and it will also be a fake wall. You'll end up at the Triforce symbol. Stand on the symbol and play Zelda's Lullaby. The water on this floor will stop flowing and drain.
Return to the pool of water you passed near the dungeon entrance. It is now an empty pit. Drop down into the pit, and you will find a crawlspace. Go through that passageway. Go forward, kill the Big Skulltula, climb the wall and go through the door.
There are several hands in this room. Go up to one and get caught by it. When a hand traps you, the sub-boss, Deadhand will appear. Tap buttons to breakaway from the hand you trapped yourself in. Ignore the hands but stay clear of them unless you need to call Deadhand back again. The hands do not harm you although they can hold you while Deadhand comes to attack. After breaking free of the hands, attack Deadhand with your sword a couple times when he brings his head down and then he will slug away. When he burrows into the ground, defend with your shield, because the dirt he shoots out will harm you. Repeat this process until he is dead.
A chest will then appear. It contains the Lens of Truth. With this item acquired, you are now free to exit the dungeon. Return to the Temple of Time. Retrieve the Master Sword and play the Nocturne of Shadow to warp to the Graveyard.
Play the nocturne of Shadow and warp to the Graveyard. Head down the tunnel behind you. Stand in the center platform and use Din's Fire to light all of the torches at once. You are now free to enter the Shadow Temple. However, once you enter this temple, you'll be entering a world of nightmarish terrors!
Once you are in, go forward and use the longshot to get past the gap. It looks like a dead end but it isn't. Just put on the Lens of Truth and go past the wall. In this room turn left and put on the Lens of Truth. There is in opening in the wall. Keep your Lens of Truth of on and stay on your right. There is another opening in the wall. Enter the door and kill the one Re-Dead and two Keese in this room to get the dungeon map. Leave the room and walk around this maze until you find another opening. Go in it and then through the next opening. You'll eventually find a door. When you do, go in it. You'll fight Deadhand again. Fight him the same way you did before to kill him. Once you do, a chest will appear like before, only this one contains the Hover Boots. These boots have built-in hovering capabilities that allow you to walk across pits and reach inaccessible areas. However, the boots have no traction and will stop working after walking on nothing too long. Now leave and head back to the main room.
In the main room there are a bunch of skulls around a bird statue. There is also a locked door that seems unreachable. It will open if you move the statue. It says to face its beak towards the skull of truth or descend into darkness. Put the Lens of Truth on and see the real skull. Now push the statue until it is aligned with the correct skull to make the door open. If it isn't, run away because the floor surrounding the statue is a trapdoor. Put on the hover boots and get to the door. Go through it. Go down the passage until you reach the Beamos. Kill it using your bombs. Go through the wall on the right and enter the door. There is a new enemy here; a Gibdo. It screech-attacks like Re-Dead do, and only attacks when you get near it, but its screeches are stronger, and so are they. Defeat the two here to get the compass. Exit the room and walk straight across. In this room there are a bunch of silver rupees and a scythe trap. Turn to your left and bomb the wall. Go through the locked door.
Go down the hallway and watch out for Big Skulltula on the way until you reach a room with falling blades. Keep going until you reach a platform. Try not to get into conflict with the Stalfos that will appear. There is a Wallmaster lurking about, so if it comes after you and it gets you, you'll end up back at the temple entrance. If you have Farore's Wind, it would be a good idea to create a warp point here. Turn to your left and put on the Lens of Truth and your hover boots to get across the area. Enter the door you come to. This room has a hidden scythe trap and more Silver rupees. Kill all the enemies in here. Then exit and go back to the platform with the Stalfos. Kill the Stalfos this time and then look to the one side that you haven't been yet. There is a moving platform. Time yourself so that when it is at its lowest point jump onto it. Jump onto the platform with the silver rupees. There is a spike trap and a Beamos. All but one of the Silver Rupees are either in the path of the spike or near the Beamos. The last one is under the Beamos. Blow the Beamos up to get that one and get the other Silver rupees to open and then enter the door. This is the giant spike trap room. Once you get in put on your Lens of Truth and look to your right. There is a block in the wall. Pull it out and then push it towards the falling spikes. Once it is holding both of the spikes so they can't hit you go around to the other side and pull it all the way. Then get on top it and jump to the top of this room. Across the room on the other ledge is a switch. Use your hover boots to get there and press the switch. Although they are moving and slanted on top, you can walk across the top of the spikes. After the switch is pressed, a treasure chest will fall. Jump down and open it, then leave the room. Go back to the platform that moves up and down. Get onto it and turn to your left this time. Go across. Put on your Lens of Truth and you will see a new platform. Get onto that and then onto the next one and go and open the locked door.
This room is very dangerous, although it doesn't look like it. Two ReDead are here, so play the Sun's Song and kill them. This will put their souls at rest, and a chest with a Blue Rupee inside will appear in return. Now, you will need to use the Lens of Truth, because columns of hidden spikes are littered throughout this room. There are also Silver Rupees you need in this room. Use the Lens of Truth to see hidden platforms and Hookshot targets to get the Silver Rupees without doing yourself any harm.
Enter the door that opens in this room. Climb up the stairs in this next room and pick up a Bomb Flower growing at the top of the stairs. Throw it in the the flaming skull pot. When it explodes, the pot will explode as well, shooting out a small key inside. Get it and kill the Keese and Fire Keese in the room to open the door so you can get out of here and back to the last room. Use the Lens of Truth on the ceiling to see a Hookshot target. Latch onto the target to land on a ledge above and enter the locked door there.
This next room is a narrow corridor filled with danger. Big Skulltula constantly drop down from above in this room. Not only that, blowing fans threaten to send you flying. Use your Iron Boots to make it through the strong winds the fans are making, or wait for them to stop and use your Kokiri Boots to run though. Go past the first fan and the spike trap, and watch for Big Skulltula in the corridor as well. Now, you'll have to cross a pit with a fan on the other side. Use either the Hover Boots or the Longshot on a wooden beam above the other side to get across. Then, you'll encounter more fans and Big Skulltula. When you get past them, you'll reach the end of the corridor, which will have a dropoff and a fan above. Switch to the Hover or Koriki Boots to jump down, because you can't jump down in the Iron Boots. Finally, you'll reach a part of the room with fans on both sides and one straight platform in the middle. Use your Iron Boots to get across. You don't need to enter the room ahead. There is an eye switch at the end that will shoot fire at you. To make it stop, blind it with an arrow. Once you get to the other side of the platform, turn to the left and use the Lens of Truth. Look to the wall and you'll see a hidden doorway. Equip the Hover Boots and run to it when the fan behind you is blowing. The extra boost from the wind will allow you to get to the door. Unlock it and go in.
In this room there is a pile of bones in the right-hand corner as so as you come in. Bomb it to destroy it and use your Lens to find a treasure chest. It has a key. Beyond you are two Gibdos and two spike traps. Play the Sun's Song and kill them, and they will leave behind a chest holding a Blue Rupee. Go past the spike traps through the locked door.
You are now in a room with a large ship. There is a block to your left. Pull it and push it along a small rut in the floor to a ladder on a nearby wall so you can reach it. Climb up the ladder and jump onto the ship. Play Zelda's Lullaby on the Triforce symbol on the ship to make it start moving. Keep an eye on your map in the corner. The moment you get the ship moving, a Stalfos will drop down onto the ship. After a while, so will a second one. Stave them off and kill them, or lead them right off of the ship. Whatever you do, don't jump into the murky water below, or you'll end up back at the start of the room.
Eventually the ship will go as far is it can. When it does, it will sink, and Navi will tell you to abandon ship. Jump off the ship and onto the nearby ledge. If you look back at the ship, you'll see the it sink completely. Enter the door that is at the end of the ledge.
When you enter this room, you will need to use the Lens of Truth. The room is actually filled with hidden walls that form a maze. The Lens of Truth will reveal them. Be very alert while you go through the maze, because a horde of Floormasters patrol the floor. The maze leads to three other doors besides the one you came from. Go through the maze and use the Compass and Dungeon Map to find a door in the east corner of the room.
In this next room, the door will lock behind you. If you look around, no enemy can be seen in this room, or so it seems. Put on the Lens of Truth and you'll see a Floormaster. Don't take the lens off, or else it will dissapear. Slash it to make it split into its smaller versions and kill them to make a chest with a small key inside appear. The doors will unlock, and you can move on.
Return to the maze and guide yourself to a door in the west corner of the room. Go in and you'll face another deathtrap: two walls covered with spikes. It may seem like there isn't a way to destroy these walls, but there is. The walls aremade of wood, so use Din's Fire to light the wood on fire and destroy the walls. However, you'll find two ReDead in the room's corners. Play the Sun's Song to stun them and then kill them. There are two chests in this room- one holds a Blue Rupee, and the other is the intricate chest that holds the Boss Key!
Go out of this room and out of the maze room completely so that you're back at the ledge where the ship sank. If you look across the ledge, you'll see another ledge on the other side of a big pit. The only problem is, you can't reach it.Take out the Fairy Bow and look around. You'll find a gargoyle statue with Bomb Flowers under it. Shoot one with an arrow to make the rest explode, which will break the gargoyle statue and cause it to topple across the pit. You now have a bridge to cross the pit. Make your way to the other ledge, and you'll find a locked door. Go inside and your journey through shadows will near its end.
This next room is the last one before the Boss room, and you can even see the door right in front of you! The only problem is, it's the only thing you can see in this room, besides the door behind you. To fix this problem, use the Lens of Truth. Several small platforms will appear. Cross onto them with the Hover Boots to make it to the Boss door. Open this door and you'll be in a dark room littered with bones. There is also a hole in this room. Drop down it to face the nightmarish Boss.
You will find yourself on a platform in the dark and see a hand come down and hit it, bouncing you up. Then another hand will appear and hit the platform. The hands will pound on the platform and then you'll find out that it is actually a giant bongo drum you are standing on. Then the giant dark monster from before will appear and will form into the body that the hands come from. This monster is the boss of the Shadow Temple, Phantom Shadow Beast: BONGO BONGO.
This is a boss that can be dangerous. If you have a Fairy or Red Potion with you, they'll come in handy. If you have the Biggoron's Sword, things will be much easier. You fight Bongo Bongo on his giant bongo drum, which is a challenge. First you will see his two hands, which will be beating on the drum constantly while the rest of him vanishes. His hands try to swat, punch and grab you, so make sure you keep an eye on both hands so that one doesn't get you by surprise. Try your best to not get knocked off the bongo, since there's a pool of sinister poison down below. If you get thrown off, climb up the side of the drum to get back up. You have to shoot both of the hands with arrowsfrom your Fairy Bow or the Longshot's extending chain. This can be difficult because you're thrown up and down by the beating of the drum, so the best time to get them is when they try to hit you. Once you have shot both of the hands activate your Lens of Truth and you will see Bongo Bongo's face. Z-target and hit his eye with an arrow or the Longshot. Be sure to do this fast, or else he'll try to ram you off the side. Then run up to him and hit him with your sword as many times as possible.
Once you've given Bongo Bongo the boot, he will pound his drum one last time and melt into poison. Don't worry; the poison evaporates. Get the Heart Container, and then you can finally leave this scary temple of nightmares.
You will be transported to the Chamber of the Sages after stepping into the blue light. There you will be re-acquainted with Impa, who has become the Sage of Shadow. After a few compliments, she tells you that you will meet the princess again soon, and she will explain everything. She grants you the Shadow Medallion , which contains her power.
A secret trick is to open all the chests on the right when you first play. They will all contain keys.
Inside the well is a room with a Fire Keese and Beamos. Go into the door behind them and there will be a Like-Like inside. Kill it to get Rupees, and open the chest to get a Hylian Shield.