After getting the Lens of Truth from under the well, you can reach the Shadow Temple.
Learn Sun's Song
It is recommended (but not required) to learn Sun's Song before you enter this temple. If you have not learned it yet, go to the grave in the back of Kakariko Graveyard and stand on the Triforce symbol and play Zelda's Lullaby. Drop into the hole that appears, and make your way through the underground area to find the sign on the wall in the back. You will learn Sun's Song when you read the sign.
Get the Map
Use the Longshot to go across the gap. When you walk toward the wall, it will say something about the lens of truth. You don't need to use it to go past, but you will need it all throughout this temple. Walk through the wall to reach the next area.
Go up to the statue in the middle of the room. The statue will tell you to point at the true skull. Use the Lens of Truth and you will see that all but one skull disappears. Be careful, because if you stop rotating the statue before it is pointing at the true skull, the floor will disappear, you will get hurt, and you will be sent back to the entrance.
After you point the statue in the right direction, a gate opens that you can't reach yet, so ignore it for now.
There are two fake portraits in the wall. Use the Lens of Truth to see them, then go into the one on the right. Then go through the door straight ahead. Approach the skull straight ahead and it will talk to you. Walk through the skull wall, then go to the right use the Lens of Truth to see the fake wall on the right. Go through the fake wall, then go through the door at the end.
Kill the Keese and ReDead to make a chest appear. Open it to get the map.
Get the Hover Boots
Go back to the skull room and turn right, and use the Lens of Truth to see a fake wall on the right. Go through it, then go straight ahead through another fake wall. Go to the right, then go left, and the Lens of Truth will show you a fake wall straight ahead. Go through it, and go through the door within.
You have to battle another Dead Hand here. Let one of the hands catch you, then wiggle the control stick and tap the buttons until you escape from the hand, then hit Dead Hand in the face repeatedly. When it turns around, keep your distance to avoid the shockwave that it creates when it goes underground. Repeat the process until it dies. Open the chest that appears. You will get the Hover Boots. This item lets you walk over a gap and float there for a few moments, but the effect wears off quickly, so be careful to only use it to run across short gaps. It also lets you walk across quicksand without sinking.
Get a Key
Go back to the room with the bird statue. Go to the edge and face the tongue where the gate opened earlier, then put on the Hover Boots and go across to the tongue. You will fall before you get there, but if you ran directly toward it, you will grab the ledge and can climb up. Take off the Hover Boots and go through the gate. Keep going straight, and you will reach a room with a Beamos in the middle. There is a fake wall to the left. Go through it, and go through the door beyond it.
There is a spinning blade in the center of the room. Don't go toward the portrait at the end of a hallway in this room, or you will fall into the invisible hole in the floor there. Collect all of the silver rupees to open a gate. The gate has a portrait above it. Go through where the gate was, then open the chest to get a small key.
Get the Compass
After you get the key, exit the spinning blade room the way you came in, and return to the Beamos room. Go around the Beamos and go through the wall straight ahead. Play Sun's Song to freeze the Gibdos. Kill them to make a chest appear. Open it to get the Compass. Then leave this room the way that you came in.
Get a Gold Skulltula
Go back to the room with the Beamos. Throw a bomb at it to kill it. You can play the Song of Storms after you kill it, and a fairy will appear where the Beamos was. Then put a bomb against the wall to the right of where the Beamos was. Then go through the locked door that is revealed.
There are Skulltulas hiding in the ceiling up ahead, so go slowly. In the N64 version, you can kill them before they come down if you use the Longshot where you can see their legs sticking out of the ceiling.
There is a ledge up ahead. Be careful not to jump too far forward off of the ledge, because there is a guillotine blade ahead. There is also a Skulltula just beyond the guillotine blade. Wait for the guillotine blade to slowly rise, then carefully go forward, and kill the Skulltula when it appears. Then wait for the second guillotine blade to fall, and go past it when it rises.
As you go farther down the hallway, Navi warns you that there is a wallmaster here. Go into the large room ahead and run around to prevent the Wallmaster from landing on you, then kill it.
Jump from platform to platform, avoiding the guillotine blades. A Bubble will attack when you approach the third blade, so be careful. After you jump to the platform beyond the third blade, a Stalfos falls from the ceiling. Kill it. You can play the Song of Storms on this platform to make a fairy appear.
Then look to the left of this platform and use the Lens of Truth to see a couple of invisible platforms that you can jump across to reach the door. Go through.
Go around the corner, but don't go into the large room. Use the Lens of Truth to see an invisible spinning blade in the center of the room. Kill the Keese and the Like Like in the room to open the gate in the far wall. Go through and kill the Gold Skulltula, then open the chest to get a blue rupee, then use the Lens of Truth to see an invisible chest. It contains a bundle of arrows. If you want to get the floating hearts in the corner of the large part of the room, play the Song of Time near them to create a block that you can climb to reach the hearts.
Get a Second Gold Skulltula
Go back the way that you came and jump over the invisible platforms to return to the platform where you fought a Stalfos before. You will have to fight another one.
To reach the platform that rises and falls, put on the Hover Boots and wait for the platform to fall as far down as it will go, then start running. Land on the platform, then remove the Hover Boots. You might want to let the platform rise and fall a couple of times to get an idea of the timing. Then when the platform rises up most of the way, run toward the guillotine blades to land on the ledge.
Don't go toward the guillotine blades yet. First, go to the left, where there is a Beamos and a couple of Razor Traps. Throw a bomb at the Beamos, then collect all of the silver rupees (one of which was under the Beamos). Go through the gate that opens, and go through the passageway to the next area.
There is a fake wall on the right that is hiding a block that you can pull. Pull it onto the portrait in the floor. Then push it toward the falling spikes. When it is under the first set of falling spikes, carefully push it forward until it is under both of the falling spikes.
The cell on the left contains a Gold Skulltula. There is a chest in the other cell that contains arrows.
Get a Second Key
Go to the far end of the room. Pull the block toward you until you can't pull it any farther, then climb up onto the block. From there, go to the ledge on the right and step on the switch to make a treasure chest fall from the ceiling. The chest contains a small key. The final chest in this room contains a blue rupee.
Get a Third Gold Skulltula
Leave this room and go back to the large room. Go to the nearby guillotine blade, then use the Lens of Truth to see the invisible platforms beyond the blade. Jump past the blade and get on the invisible moving platform, then jump from there to the door. Go through.
First, play Sun's Song to freeze the ReDeads. Turn on the Lens of Truth to see the invisible spikes in the floor (you can wear the Hover Boots to walk safely over the spikes), then kill the ReDeads. When the ReDeads are gone, a chest appears. It contains a blue rupee.
Then collect the silver rupees in the room. You will need to use the Longshot to reach the floating rupees. Position yourself so that the silver rupee is between you and a Longshot target, then use the Longshot on the target to be pulled through the rupee. For one of the silver rupees, you will need to use the Lens of Truth to see an invisible target on the ceiling above the platform with the locked door on it.
After collecting all of the rupees, go through the door that opens.
There are four Keese in this room. Go behind the giant skull and kill the Gold Skulltula there.
Get a Third Key
Go up the stairs and throw a bomb flower into the skull. After it explodes, take the small key that comes out.
Kill the four Keese in the room if you haven't already. The door will open. Go through.
Get a Third Key
Use the Lens of Truth to see the invisible target above the locked door. Use the Longshot on the invisible target, then go through the locked door.
Go through the passage until you see a fan in the wall. Put on the Iron Boots so you can contiue walking through the passage without being pushed back by the fans. Kill the Skulltula that comes down from the ceiling. When you reach the gap, use the Longshot on the piece of wood in the ceiling to get across.
In the area with the fans on the sides, be careful of the flames that come out of the eyeball above the ceiling. Don't bother shooting the eyeball, because it has no effect. You can raise your shield to block the flames.
There is a fake wall across from the fan at the end of the room. While still wearing the Iron Boots, walk into the path of that fan, wait for the fan to stop, then put on the Hover Boots. When the fan starts blowing again, run toward the fake wall. Go through the door that you find there.
Play Sun's Song to freeze the Gibdos, but be careful of the flying jars near the Gibdos. Kill the Gibdos to make a chest appear. It contains 5 rupees. Then bomb the pile of skulls in the corner near the door where you entered the room. There is an invisible chest there that contains a small key. Use it to go through the locked door.
Get a Fourth Gold Skulltula
There is a ghostly ship in this room. Go to the left and pull the block to the path in the center. You can climb the chains on the wall and break the jar to get a fairy, but don't climb up the next set of chains, because it goes up to a room that you have been to before, and the block that you pulled might go back to where it started, preventing you from returning directly to the room with the ship.
Go back to the block and pull it along the path, toward the ladder. Go around to the other side of the block and push it into the hole in front of the ladder. Climb onto the block, then climb the ladder. At the top, play Sun's Song to reach a Gold Skulltula on the other side.
Get the Boss Key
Go back down to the block, climb it, and climb the ladder. Jump onto the ship, then stand on the Triforce and play Zelda's Lullaby. The ship will start moving.
Stalfos will attack when the ship starts moving. Battle them, but when the ship reaches the end, jump off, because it is about to sink. Go through the door on the right.
This room has many Floormasters, and there are invisible walls blocking your path. Go counter-clockwise through the room. If you kill a Floormaster, use Din's Fire right afterward to kill the small hands. They always drop magic jars, helping to refill your magic meter afterward.
Go through the door on the right (in the north wall) and use Din's Fire to burn the spiky wooden walls that start closing in on you. Then play Sun's Song to freeze the ReDeads, and kill them. Open the big chest to get the Boss Key. The small chest contains a blue rupee.
Get a Fifth Gold Skulltula
Leave the room, then make your way to the door in the west wall. There are three spinning skulls in here. Go behind the skulls and kill the Gold Skulltula there. The skulls themselves just contain rupees, so you can bomb them if you want, or just ignore them.
Get a Fourth Key
Go back to the Floormaster room and make your way to the door in the south wall. Go through, then use the Lens of Truth to see the invisible Floormaster. Kill it, then use Din's Fire to kill the small hands. Open the chest to get a small key. Then go back through the east door to return to the room where you rode on the ship.
Go to the Boss
Go past the statue, and stand between the two pots up ahead. If you look across, you see that the statue beyond is surrounded by bomb flowers. Use an arrow to light one, and they will all blow up, causing the gigantic pillar to fall, which allows you to cross the pit. If you want the hearts, play the Song of Time to get one of them, and play Scarecrow's Song to get the rest. Otherwise, go through the locked door.
Put on the Hover Boots, turn on the Lens of Truth, and make your way across the platforms to the door. Try going straight ahead from the door to reach the T-shaped platform, then go to the platform on the left, then go to the platform near the door, and finally go to the door. Go through and drop down the hole to face this dungeon's boss, Bongo Bongo.
Bongo Bongo's disembodied hands will hit the bongo that you are standing on. If you stand on the edge of the drum, you won't bounce up into the air when the hands hit the drum. Shoot the hands to stun both of them. The hands are only vulnerable when they are open. After the hands play a rhythm, they will try to pick you up and crush you and throw you, so try to stun them as soon as possible.
When both are stunned, activate the Lens of Truth to see Bongo Bongo's body. Shoot its eye with an arrow before it hits you. Then run over to Bongo Bongo's eye and hit it repeatedly with your sword.Note that your arrows will fall back onto the bongo, so be sure to pick some up if you can safely do so. Magic jars will sometimes appear as well.
Repeat the process until Bongo Bongo is defeated.