NOTE: This Walkthrough will cover, each and every Heart Piece, Item, Boss, and everything else.
From just outside Swamp Palace, head right a screen and up two screens. Head right a screen once again here and pound the stakes with the hammer. Head up two screens and kill the two enemies here. At the top of this area you will notice a skull, a stake, and a rock. Just above the stake you will notice a small area against the water. Go there and use your hookshot to hook across the bridge. Head up a screen.
Head left three screens and up one more. Go to the top-right of screen and lift the rock here. Enter the cave. Kill the two enemies if you wish and then head up the stairs. Go down a bit and use your hookshot to get across the hole in the ground. Go down and you will see a bumper. Use your magic cape to go through it. Take off the cape once you are through and exit the cave. Grab the quarter heart container and then jump down from the cliff.
Head down a screen, left a screen, and then up a screen into Skull Woods. Head up and fall into the first hole that you see to enter the actual dungeon. From where you land head down. You will notice a treasure chest. Lift the pots and open the chest for a small key. Be acreful htat the wallmaster does not grab you. After you have the key go to the top-right of the screen and go through the locked door.
Step on the stars and then open the treasure chest at the top-right to get the Dungeon Map. Exit to the left. Head down and out to be back outside. Head down and left and you will see another hole. Fall down.
Make your way down this room and exit to the right. Head up here and open the chest for the Compass. Once Link gets the compass the ground will drastically change. Afterwards head up a screen.
Kill all the enemies in here. Open the trasure chest at the top-right for anoter key. Head right a screen and you will notice you are back in the Big chest room. Head out through the bottom once again.
Back outside again head to the top-left and go through the passageway. Make your way around until you come to another entrance. There are a couple enemies in here, including a wallmaster. You can use bombos to get rid of all of them at once. The wallmaster will keep coming back. There is a switch under the pot in the middle of the room. You must pull the statue on the right side onto the switch to keep the door opened. You have to pull it or else you will not be able to reach the door it unlocks at the top.
Head up a screen. There are a bunch of enemies here as well. You can use bombos to kill them all at once. Open up the treasure chest in the middle to get the Big Key. You can bomb the wall to the right to get some magic if you need to. Pull out your magic mirror and use it to get back to the entrance of this part of the dungeon. Leave this part of the dungeon and make your way back to the other side on the right.
You will notice nine bushes. Cut through the reveal a hole under the middle bush. Fall down the hole. Lift all the pots here to get some items and hearts. Afterwards place a bomb on the left wall. Before going through to the left, step on the first set of stars.
You can hookshot across if you would like to lift the pots for some magic power. Afterwards pull the switch in the middle. The wall on the bottom will explode allowing Link to walk through.
Kill the two enemies here and then open the chest to get the Fire Rod. After getting the fire rod go to the left or right side and hookshot to the bottom to grab onto the statues. Then exit through the bottom. Once again make your way to the top-left and get to the other entrance.
Head left two screens. At the top-left of the screen there is a jar. Lift it to get another small key. The locked door above you can be reached if you go outside and go up on the right side and fall down a hole. You can step on stars to change the location of the ground holes, but the room is a trap and is useless to enter. The extra key will make things easier in this next part of the dungeon. Exit to the bottom.
Once you are outside go through the area at the top-left. You will notice a huge skull with something hanging down. Use your Fire Rod to light the thing hanging down the skull the open up the entrance to the final area of the Skull Woods. You will notice a terasure chset here. It contains a small key, but since we kept the one from th previous part of the dungeon, you do not need to go through the pain of getting that one. Head up and through the locked door at the top.
This maze is annoying. Head up ot the middle of the room stepping on the stars. Then step on the star at the bottom-left. Head around and step on the stars on the right side. Then step on the star at the top-right. You should now be able to access the door. Head right a screen. The four gibdos in here are a pain because they take a bunch of hits to kill. You can kill them one by one of all at one time with bombos. Lift the two pots on the right side. Then quickly light the bottom lantern, and the two on the sides with the lamp. Head up and light the top one with the fire rod and then head left.
Use bombos once again to quickly kill all the enemies here. Slash the top to reveal a passageway. Head up a screen.
Kill all the enemies and grab the key that is left and go through the door on the right side. Lift the pots to get some magic here and an arrow and then fall down the hole to fight the boss.
Mothula can be a real pain. It takes 15 hits with the Master Sword, or 10 hits with the Fire Rod. Be careful of the moving floor, the spikes, and the beems that are shot out at Link. It is a good idea to have a fairy or two in your bottles just in case you die.
After you have defeated Mothula grab the full heart container.
Also grab the 3rd crystal. The maiden in the crystal will talk to Link about more of the Triforce and how Link is the hero that needs to save Zelda and the Golden Land. You will then be teleported to just outside of the dungeon. Afterwards head down and head back into the dungeon. Head right two rooms and leave the dungeon. Make your way around to the right side of the dungeon. Head all the way to the bottom-right and out of Skull Woods.