Once you warp to the Graveyard, walk down the stairs and there will be numerous torches that are unlit. Stand on the small platform in the middle of all the torches and use Din's Fire. This should light all of the torches. The door leading into the temple will open. Walk into the temple and to your right, is a large gap. Use your Longshot to make it across. The wall directly ahead of you is an illusion so walk right through.
Skull Room
Only one of the skulls in this room are real, use the Lens of Truth to find the real one. Grab the statue and push it around until it is pointing at the real skull. When it is pointing to the real skull, an opening is revealed across the large gap. Use the Lens of Truth to find another illusion in the back, right corner.
Map Room
Make your way through the passageways with the Lens of Truth to find a room with a Re-Dead. There are also two Keese that you must kill. When you kill the Re-Dead, the chest with the map appears.
Hover Boot RoomOnce you have that, you must use the Lens more to find another hidden room. The next room that you enter will be nearly identical to one room you found in the Bottom of the Well. Six hands will be rising from the ground. Go near one and let it grab you. The main part of the creature will come out of the ground. Hit the buttons rapidly to get away from the dead hand. Let the creature come towards you and just when it is about to bite you...Slash it. After three hits it will retreat back to the ground. Repeat the process of letting the hand grab you and slashing the creature. When it dies, the chest holding the Hover Boots will appear! Head back to the Skull Room now. Use the Hover Boots and a running start to get across the large gap. Link should just make it and climb up.
Beamos Chamber
Walk down the hallway and you'll come to a room with three exits. Either avoid the Beamos and walk around the edge or kill it with a bomb or two. One of the three exits are locked and you have no key. Enter either one of the other two doors.
Gibdo Room
As soon as you enter this room, play the Song of the Sun to freeze the two Gibdos. Kill each one. If one happens to attack you, hit the buttons rapidly to get away! When both are defeated, the chest holding the Compass appears. Leave this room and go into the other unlocked room.
Spinning Blade Room
As you enter this room, a large blade spins around the room. Like a room in the Ice Cavern, you must collect 5 Silver Rupees in here. Use your skills and items to get all of the rupees. Once you get all five, you can get the small key from the chest in the niche. Head back to the Beamos Room and unlock the door.
Guillotine Trouble
Go through the passage way and kill the big Skulltulas. Take a left at the end of the hallway and you'll come to a ledge with a Guillotine. Jump down and watch the pattern of the blade. Roll past it when it goes back up. You must do the same for the rest of them too! Time your jumps and roll carefully and watch out for the gaps near each guillotine. At one platform, a Fire Bubble will fly towards you. Do a backflip or block with your shield. On the final platform, a Stalfos will pop up. Defeat it and take out the Lens of Truth. To the right, a platform is being raised and lowered. Don't go there yet. To your left...nothing...unless you use the Lens of Truth.
Use the Len of Truth to find a path along the wall. Wear the Hover Boots to make the jumps easier here. Enter the door walk down the hallway. You'll come to a large room and you'll see a Like-Like on the other side. Use the Lens of Truth to reveal another large blade spinning around the room. Kill the Like-Like with arrows so you don't have to take a chance of losing your shield. Walk around the edge of the room and kill the three Keese here to raise the bars blocking the Gold Skulltula. Get the Gold Token from the Skulltula and head back to the platform where you fought the Stalfos. Another Stalfos pops up when you set foot on the platform again. Defeat it and equip the Hover Boots. When the platform to the right is as low as possible. Run and hover over to the platform. Jump to the next platform and kill the Beamos. Collect all the Silver Rupees to open the gate blocking the door. Enter the door when the gate rises.
Spike Crushing Platform Room
In this room, there are two large platforms which are covered in spikes. If they hit you, you'll lose one whole Heart Container of life and start at the beginning of this room. Use the Lens of Truth to uncover a hidden crescent block on the wall to your right. Pull it out and begin pushing it across the room. When it is blocking both of the spiked platforms from coming down, get on the other side of it and continue by pulling it. When you pull it as far as possible, climb up and jump to the ledge on your left. Hit the switch to make a chest drop on the other ledge. Target the chest and Longshot over to it. There is also a Gold Skulltula in a cell here. Leave the room and kill the Beamos again. In the corner, a narrow walkway leads to the next doorway. Walk along the platform and get past the guillotine. Use the Lens of Truth to reveal a hidden platform past the guillotine. Jump onto it and equip the Hover Boots to make the next part easier. With the Lens of Truth, you will see a moving platform. Hover over to the door when the platform is directly across from it. Enter the door.
Spike Floor Room
Hint: Use the Hover Boots and you'll automatically hover over the spikes. As you enter this room, you will see Silver Rupees throughout the room. Kill the Re-Dead and collect the rupees by using your longshot. The Silver Rupee that is in the center of the room looks unreachable. Use your Longshot to pull yourself to a target while you're lined up with the rupee. This way, you'll grab the rupee when you are pulled up! When you collect them all, enter the room on the left wall.
Skull Vase Room
As you enter this room, you will see a large skull vase rotating on a platform. You must kill all the Keese before you can leave the room. Climb up the side of the room and grab a bomb flower. Throw it into the vase as it comes by you. It may take a few tries to blow it up. Once the vase blows, a small key is revealed. Grab it and kill the Gold Skulltula on the wall. Head back out to the Spike Floor Room and use the Lens of Truth to find a hidden Hookshot target above the platform with the locked door. Longshot up and enter the door.
Wind Tunnel
Hint: Use the Iron Boots so you don't blow away! Go down the hallway and turn to the right. You'll see two Razor Traps and a large fan at the other end of the corridor. You are supposed to wait for the fans to stop so you can walk without being blown away but using the Iron Boots is easier. Equip the boots and begin walking through the hallway. When you come to a gap, use your Longshot to pass over it. With the Iron Boots on, you won't blow away! The next room has a walkway through the middle and fans on each side. Use the Iron Boots here too! The eye above the door is not like others...it doesn't open doors when hit. Instead, it will spit a ball of fire out at you. Block it with your shield. Instead of entering the door at the other end, use the Lens of Truth to reveal a hidden niche on the left wall. Line yourself up with the fan and equip the Hover Boots. When the fan starts up, it will blow you nearly all the way across. Use the Hover Boots to get in.
Gibdos and Razor Traps
As you enter this room, blow up the pile of junk to your right. Use the Lens of Truth to reveal a hidden chest with a small key there. Defeat both Gibdos by playing the Song of the Sun and slashing them to death. Open the chest that appears. Unlock the door on the other side of the room now.
Floating Ferry Room
When you enter this room, save some time by using your Longshot to get up the ladder to your right instead of pushing the crescent block all the way down here. Make sure you're lined up with the ladder and not on an angle and hold up on the control stick so Link will climb up. From this platform, play the Scarecrow's Song when Navi turns green on the far side of the room. Longshot over and get the Gold Skulltula and the recovery hearts if you need them. Head back over to the other platform and jump onto the ferry. Stand on the Triforce crest and play Zelda's Lullaby. The ferry will begin to move and a Stalfos will attack you. Defeat it carefully...Don't fall off! When Navi says the ship is sinking, jump to the walkway on your left. Enter the door at end.
Floormaster Room
As you enter this room, use the Lens of Truth to reveal hidden walls everywhere. Two Floormasters guard the area so kill them when you find them. Going by the map in the bottom right corner, head for the room to the south. Use the Lens of Truth to find a hidden Floormaster in here. Kill it before it kills you. Next, head for the room to the west. Grab the Gold Skulltula behind the spinning vases and break the vases to get some rupees or hearts if you want. Finally, head for the door at the north end of this room. When you enter this room, spiked walls begin closing in on you! When they are fairly close to you, use Din's Fire to burn them to a crisp. If you're out of magic, break the pot near the wall! Kill the Re-Dead and get the Boss key from the chest. Now, head back to the room where you jumped off the ferry.
The Final Steps
It seems there is no way to go but there is. At one end of the walkway, look over across the gap to see some bomb flowers. Shoot one of them with an arrow to make yourself a bridge. Walk over and play the Scarecrow's Song to get the recovery hearts on the platform high above. For the other hearts, play the Song of Time when Navi turns green. Enter the door and use the Lens of Truth to find the hidden platforms in here. With the help of the Hover Boots, you can make your way to the boss arena. Enter the boss arena and fall down the hole.
Phantom Shadow Beast:Bongo Bongo
You will land on a drum and Bongo Bongo's hands begin hitting it. You have no control over yourself and you bounce with the drum. Lock onto one of his hands and shoot an arrow at it. He will try to hit you with the other hand so either quickly hit the other with an arrow or avoid being hit. Once you hit both of his hands, use the Lens of Truth to find his eye. When he rushes at you, hit his eye before he hits you. If you hit him, lock on and slash him as much as you can. If he happens to grab you with one hand, he'll squeeze you with all his might and hopefully, you have a red fairy or lots of life. If you fall off the drum, climb back up quickly! Hit his hands again and slash his eye when he comes at you. Eventually, he'll die. Grab the Heart Container and step into the light. Impa will tell you that Zelda is alive and well. She also tells you that you will meet her face-to-face soon. She will give you the Shadow Medallion. You need only one more now! Head to Gerudo Valley now. By the way, on a side note I would just like to add that you'll love the music in Gerudo Valley.....IT ROCKS!!