This place is seriously creepy, even worse than under the well.
Use your longshot to get across the gap (the gap is there to prevent you from getting into the temple as a kid). When you walk toward the wall it will say something about the lens of truth. You don't need to use it to get past, but you will need it all throughout this temple. You can just walk through the wall to the next area.
Enter the Temple
In this room, there's a weird bird statue in the center of some pillars with skulls on them. Go near and you're told you have to point at the true skull. Use the lens of truth to spot the real skull (the others disappear when viewed with the lens), then start pushing the statue and DON'T STOP until you're pointing at the real one or the floor will disappear and you get hurt and sent back to the beginning (which isn't terrible, but should still be avoided). Once you've got it right, a gate across the room goes up, but you can't reach it yet. Ignore it for now.
In the wall to the left of where you entered is a fake wall. It's in the same wall as the passage where you entered, just to the left. Just walk into the creepy face portrait to go through.
Go through the fake wall. The fake walls in this area will have green eyes, although up ahead there's a real wall with green eyes to throw you off. At the fork, make a right. There's a fake wall to the right in the center of the wall so go through it. You have to kill some keese and a ReDead to get the map. Go back out, then make a right and go through the wall to the right, also in the center of the wall. Continue through the next fake wall. From here, make a right, then go straight ahead through the wall in the corner of the room.
In here is a second Dead Hand. Kill it as before to win the Hover Boots. This item lets you walk right over a gap for a few seconds. Just be warned that its effect wears off after a few seconds, so don't go trying to walk across large gaps or you'll fall to your doom. It also lets you walk over quicksand without sinking. If you try walking on a regular floor with them, it will be like you're walking on ice.
Go back out and return to the room with the bird statue. Use the hover boots to float across the gap towards the tongue. You'll fall before you get there but if you aimed right you'll grab the ledge and can pull up and go through the door. Continue down until you reach a room with a beamos. Exit left through yet another fake wall.
An evil spinning blade is going around in the center of the room. Collect all the silver rupees to open a room with a chest containing a small key. Nothing else to do here, so exit the way you came in.
Go around the beamos and through the wall straight ahead. In this room there are a couple of Gibdos; use Sun's Song to stop them in their tracks and kill them, revealing the chest containing the compass. Go back out.
The wall to the right from the direction your facing can be bombed. Bomb the beamos to make sure it doesn't zap you while you try to bomb the wall. Once you've gotten rid of the wall, go through the locked door. Go slowly through this passage; there are skulltulas hiding in the ceiling (somehow). At times you can see a bit of their little legs through the ceiling, so if you spot one before you reach it, longshot the ceiling to try to destroy it. Otherwise let it fall and kill it then.
A little ways down you encounter some guillotines with a skulltula that attacks in between them, so wait for the blade to come down, walk into it, and you walk past it to safety when it goes back up.
Once you enter the large room, Navi warns of a wallmaster. Let it fall, and kill it. Then jump your way across the platforms past the guillotines (careful of a bubble that hops across one of the platforms). When you get to the safe (or should I say "safe") platform, a stalfos attacks, so kill it. If you turn left, you see a platform but no way to get there. Break out the lens of truth to reveal some more platforms. If you aren't collecting gold skulltulas you can skip this part. Jump to the door.
Inside, turn the corner and DON'T MOVE, but kill the Like Like with arrows first. Then turn on the lens of truth to learn the terrifying truth: there's an invisible spinning blade here. Break out your arrows to pick off the keese hanging around the walls. They're hard to see so you may have to go around looking for them. Once they're all gone, a door in the far wall opens. The room contains chests with a couple of useless items (one invisible), as well as a gold skulltula. Collect the token (to get the floating hearts you can play the Song of Time to reveal a blue block underneath the hearts) and return to the large room, making your way across the invisible platforms.
Kill the stalfos again. To get onto 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. To get to the safe area across the way, keep the hover boots on and wait for the platform to be about mid-way up, not all the way.
Once safely across, avoid the razor traps and bomb the beamos. Collect the silver rupees (one of which was hiding inside the beamos). Go through the door that opens.
In here, the first thing you need to do is grab a block that's hidden behind a fake wall to the right. Pull it out so you can push it down the hall with the falling spiky things. Push the block straight ahead until it's under the first spiky thing. Then carefully push it some more so it's between the two spiky things and they both fall on the block (as opposed to falling on you). Before proceeding, go into the cell to the left to find a gold skulltula. Then head to the far end of the room. Pull the block to the end of the path and jump onto it, then jump up to the ledge to the right. Step on the switch to reveal a chest containing a small key. Use your longshot to reach it. There are other chests here with useless items or a few rupees, get them if you want. Now you're done with this room, so go back out.
Slowly walk across the narrow ledge to a platform with a guillotine. It appears there's no way to get across to the door, but you know what to do. Once you can see the invisible platforms, avoid the guillotine and hop to the stationary one, then jump on the moving one to get to the door. Go through.
Keep the lens of truth on in here, since there are invisible spikes on the floor. Use Sun's Song to immobilize the ReDeads, kill them, and kill any keese hanging around. Collect all the silver rupees by using the longshot on various targets such that you are pulled through each rupee. For one of them you need the lens of truth to see an invisible target on the ceiling above the platform with the locked door on it. Go through the barred door that opens.
There's a gold skulltula in here behind the giant skull. Getting rid of the keese, go up the stairs and toss a bomb into the skull. It will explode and a small key will pop out, so get it. Then leave.
Back in here, use the invisible longshot target on the ceiling to get to the ledge with the locked door. Go through.
There are some fans in this hallway that will try to keep you from progressing. The iron boots counter the effects of the wind, so put them on and start walking. A skulltula will attack along the way and you'll need to use the longshot to get across a gap.
In the room with the fans to either side, the eye at the end shoots fireballs. You can't stop it doing that so just avoid the flames. Your shield will deflect them. The lens of truth will reveal a fake wall in line with the third fan. You need to walk into the path of the third fan (the iron boots will make life easier to get there). Wait for that third fan to stop, switch to the hover boots, then time it so when you make a running start with the hover boots at that fake wall, the fan will start up again, propelling you into the wall. Once you've done it right, exit.
Play Sun's Song and defeat the Gibdos to reveal a chest containing 5 rupees. There's a pile of what are supposed to be skulls (I think) in the right-hand corner by the door you entered, bomb it and there's an invisible chest there holding a small key. Exit.
There's a ghostly ship in here, meaning you're getting close to being done with this awful dungeon. There's a block to the left, pull it to the center, then over to the gap by the ladder. Climb up. If you use Scarecrow's Song up here, you can reach a gold skulltula. Once you get it, get back to the ledge by the ship. Jump onto it, and do what you always do when you see the Triforce symbol: play Zelda's Lullaby.
Stalfos will attack once the ship starts moving. Stave them off until the ship gets through the long passage to an area where you can jump off. Don't hang around on the ship because it's about to sink into the infinite depths below. Jump down, and go to the right where there's a door.
Lots of gross wallmasters in here, and what looks like an open room is actually filled with invisible walls to keep you from progresing. Make a counterclockwise circuit of the room, beating wallmasters as you go. Use Din's Fire a couple of times for a quick kill (they always leave magic jars, which makes up for the magic you consumed using Din's Fire).
The room to the right of where you entered (in the north wall) has a couple of wooden spiky things that want to impale you. Use Din's Fire to burn them to a crisp (as well as ignite the rotting ReDeads). Play Sun's Song to stop the ReDeads and kill them, then grab the chest for the boss key. Go back out to the wallmaster room.
The room to the right of this (straight across from where you entered, in the west wall) houses three spinning skulls, as well as a gold skulltula behind them. None of the skulls actually hold anything of value (well, rupees) so just grab the gold token and ignore them, and go back out.
Make your way to the one door you haven't tried yet, in the south wall. Turn on the lens of truth because there's an invisible wallmaster in here, kill it any way you like (Din's Fire is good, as I said) and get the chest for a small key. Now exit, and make your way out to the big room where the ship was.
Go past the statue, and stand between the two pots. If you look across you see that the statue beyond is surrounded by bomb flowers. Use an arrow to light one, and they'll all blow up causing the gigantic pillar to fall, allowing you to cross the pit. If you want the hearts, play the Song of Time for one, and Scarecrow's Song for the rest. Otherwise exit through the locked door.
Pull on those hover boots, turn on the lens of truth, and make your way across the platforms to the door. Go through and drop down the hole to face this dungeon's boss, Bongo Bongo. (Goofy name for such a scary-looking boss.)
Activate the lens of truth right away, because you can't see Bongo Bongo's body otherwise. It has two disembodied hands that drum the bongo you're standing on. After pounding out a rhythm, the hands will start moving around trying to push you around or crush you or do other Bad Things&trade. Your goal is to disable both hands with arrows. Stand on the very edge of the bongo so you don't get drummed into the air while the hands drum out the beat, and target the hands to hit them with arrows. Note that you can't hurt the hands while they're curled into fists. Once you take out the hands, the giant eye at the end of Bongo's neck will open (gross), and you can target it and shoot it with an arrow. His body will fall down and you have to run to it (let go of Z so you run more quickly) and start chopping away at Bongo's eye. NOTE that whenever you shoot an arrow and it hits something, it will fall right back onto the bongo and you can collect it and use it again. The arrows that land are worth more than just one arrow. Magic jars will also land if you run out of that, but you shouldn't. Repeat the process until Bongo melts into a shadowy puddle of evil. Grab the heart container and walk into the light to get the Shadow Medallion.