You need the Lens of Truth in here. Walk forward and get past the cliff with your Longshot. Turn on the Lens of Truth now. Walk through the face block. Now you're in a room with a lot of faces, use the Lens of Truth to find the one that goes to another hall. Use the Lens to find the correct path. Kill all the ReDead and Keese and you'll as a prize, you'll get the Map. Now go back into the room with the orange faces to find another path. Soon you'll find the Dead Hand mini-boss. Now you will get Hover Boots. Return to the room with the blue faces and the bird statue in the middle. The inscription reads "Make my beak face the skull of truth The alternative is a descent into the deep darkness below." 

Take out the Lens of Truth and you'll find that most of the skulls in this room are fake, except one. Grab the statue and point it to that Skull. A door will unlock. Use your Hover Boots to get there. There are three ways to go: forward, left, and right. Two are invisible, and ahead of you, you have to use a bomb on it. Go left first. You have to collect all of the Silver Rupees while dodging the spinning blades of the two grim reaper statues. You will get a Small Key. 

Now, go through the right passage. Kill the two Mummies and you'll get the Compass. Now go back and bomb the forward passage and go through the locked door. Now you have to go down a long hallway. Giant Skulltulas will drop from the ceiling so watch yourself. At the end you'll enter a large room. Dodge the guillotines and use the Hoverboots to get to the platform that goes up and down using it's chains. Now drop down to the next platform by using your Hoverboots when the platform is at it's highest. Collect the Silver Rupees to unlock the door. Go down the hall, now you'll have to go through these falling spikes. Use your Lens of Truth to spot a block in the wall, use it to get through. When the second platform starts falling on it, switch to the other side to avoid getting hit by the first one. 

At the end it will create a little ladder for you to the above area. Use the spiked platforms as bridges to the other side, just be careful, you have to time it right or else you'll be stabbed. On the other side is a switch, stand on it to activate a chest on the opposite side. You'll need to use the Hover Boots. Inside is another Small Key. No go back outside. Go up the path to the left. Use your Lens of Truth to spot the invisible platforms. Go through the locked door, you may need to use the Hover boots on the last platform, though, since it's moving back and fourth. Inside you can kill the two ReDeads for a Blue Rupee chest. Collect the Silver Rupees by using your Lens of Truth to spot spikes and invisible Longshot targets. 

You'll need to line yourself up with them, then fire your Longshot in order to get them. One will require to use your Hoverboots in the platform in the corner. When they are collected the door will open. Go up the stairs and grab a Bomb Flower, then hurl it into the flaming skull. When it explodes the skull will to, and a Small Key will be your prize. To open the door you'll have to defeat all of the Keese in the room. Go back to the previous room. Use the Lens of Truth to see the invisible Longshot target. Get there, unlock the door. In this hallway are a lot of blades, and there are fans that will try to blow you into them. 

Put on your Iron Boots to avoid that. After a while you'll find a gap with a fan across it. Above it is a log, use the Longshot to get over there. Now you'll find a bridge, with fans on either side, and an enemy eyeball that shoots fire. Kill it by shooting an arrow into it when it opens. Use the Lens of Truth to find a passage in the wall. It's too far away, even for the Hover Boots. Look closely at the fan behind you, when it is on at it's fullest, run off the cliff towards the passage (Hoverboots equipped, duh), and you should make it. Kill the two mummies for a chest with Rupees in it. Then bomb the pile of dirt near the entrance. Inside of it is an invisible chest. inside that is a Small Key. Use it to leave the room. 

The ladder is too high to reach, so push and pull the block against it to make it reachable. Up there is a boat. get on the Triforce Symbol and play Zelda's Lullaby. The boat will start to go down the river. Along the way you'll fight two Stalfos. At the end, whether or not they are both dead or not, the ship will start to sink. Jump off the port side (left). Go through the door. Turn on the Lens of Truth. This room basically a big maze filled with Floormasters. They can't pick you up, they're on the floor, not the ceiling, so you don't have to worry about being picked up and taken to the beginning. There are three doors. One has a bunch of rotating skulls, you can get a few items in there. One has a blood stained floor, use the Lens of Truth to find the invisible Floormaster. 

Kill it to receive a Small Key. The last has two walls with spikes that will attempt to crush you. Just use Din's Fire to burn them down. Kill the two ReDeads for a few Rupees, then open the sparkly chest for the Boss Key. Once you have all the keys you need, return to where you fell off the ship. Look across the gap and you will see a tall statue surrounded by bomb flowers. Take out your Fairy Bow and shoot a flower with an arrow, they will all explode and the statue will fall, making a suitable bridge. Unlock the door. Use the Lens of Truth to see the invisible platforms, and use the Hoverboots to cross them. You now be at the Boss' Door. Make sure to leave the Hoverboots on when you enter. You'll fight a rather strange, but easy, boss, Bongo Bongo........