NOTE: This Walkthrough will cover, each and every Heart Piece, Item, Boss, and everything else.
Now that Link has all three of the Pendents, he can head over to the Lost Woods and get the Master Sword. Jump down the first cliff here and then head all the way to the left where the long stairs are. Jump down and then take the cave to the left of the stairs.
Head up, the path will turn a bit, but just continue along the path. Avoid the holes and kill the enemies. Head left to the next room. Go left and down and exit the cave. Jump down the cliff and head up a screen. GO all the way to the top-left and then head left to enter in the Lost Woods. Head down left and go down a log, then go up the log just to the left of it. Head left and go through the log there. Go left and through the next log. Head all the way to the left and head up the log here.
Head up and you will see the Master Sword. Go around and lift it up. You will be contacted by Zelda, and she will tell you that with the Power of the Master Sword, you can defeat Aghanaim. Now head back down out of this area.
Once you exit, you will be contacted by the Minister, and he will say that the soldiers are coming to the Sanctuary. Head through the lost woods again and exit from the same entrance in which you came in from. Head down two screens, and then head right a screen. Head right a bit and then up and into the Sanctuary.
Head up and talk with the minister. He will say that the guards have taken her to the Castle and then he will disappear. Exit the Sanctuary.
There are a few items that Link can noe get. Head left and up a screen and enter the cave that goes up Death Mountain again. Go through the cave again and then head around and up the long stairs again. Go through the portal here and then use the mirror at Spectacle ROck once again. Head up and then left accross the bridge here. Use the book to read the stone here, and it will say to hold the Master Sword. Link will do that and Link will recieve the magic of Ether. Now head right, jump down the cliff, head all the way to the left and go down the long stairs. Go through the cave here again to get off of Death Mountain.
Head down two screens from here. Now head right a screen. Head around the Castle and head right again. From here head down two screens Go down the ladder and into the water. You will noticed an island here, just swim down and right from there. There is another island, but there is a ladder to climb up on thiss one. Enter the cave here and head up to the pond of happiness. It will ask if you would like to throw in rupees. Throw in 20 rupees. Wait about five seconds and go to the pond again, and throw in another 20 rupees. Keep throwing in rupees until it is at 100. Then a fairy will come up and will ask you if you would like to carry more boombs or arrows. Choose whichever you prefer.
After five seconds again, go to the pond and throw in 50 rupees this time. Once it is 100 rupees, the fairy will come up and let you upgrade again. Keep doing this until you are out of rupees. Remember this place in the future so you can come and upgrade some more. Leave the cave and then jump back into the water. Head up and left and climb the ladder out of the water.
Head up two screens, and then left a screen. Lift the rock and head left a bit. Head up into the Castle courtyard. Now head up into the actual castle. Head left a screen and up the stairs. Then exit the castle from the exit there. You will now be on the roof of the castle. Head right a bit and you will see the entrance a door that is being blocked by a beam. Hit it with the Master Sword. Now enter into Hyrule Castle Part 2.
Once you enter the dungeon, head up a screen. Kill the two Ball n Chain troopers and head right a screen.
Kill the two soldiers here and open the chest for a Small Key. Go through the locked door at the top. Kill the two enemies in this room, and head left.
In this maze room, head up, all the way left, and then down a bit. Once you see a torch, light it so it will make it easiar to navigate the room. Lift the pots for some hearts, magic power, and some rupees. On the left side of the room there is a treasure chest. Make your way towards it and open it for a small key. If the lights go out lite another torch. Make your way down and through the locked door on the right. Kill the two soldiers in here and go up the stairs.
Kill the two enemies in this room and head left a screen. Head left until you see a torch. Lite it to make it easiar to navigate the room. Lift the bottles for some items and head up. Kill the soldiers in your way and head right a screen. Lite the torches and kill the there enemies in here. One of them will be holding the key. Grab it and head up through the locked door.
Kill the four enemies in here and head left a screen. Kill the two red soldiers and head down a screen. There are four enemies in here. The red soldier on the inside holds the small key. Lift all the pots and kill all the enemies. Now head right a screen. Kill the three enemies here and head up the stairs.
Push the statue on the left to the left a bit. Kill all the enemies and head left a screen. Kill the two soldiers here, while trying not to fall. Head up the stairs.
Once you are in this room, the music will change. It signals that you are very close to Aganhim. Head up a screen.
You will see Aganhim and Princess Zelda here. Agahnim will vanish Princess Zelda, and after a brief conversation will leave the room. Head to the top of the screen, and slash through the middle curtain. It will reveal a passage. Head through it and prepare to battle Aganhim.
After some trash talking from Agahnim, the battle will begin. In order to defeat Agahnim, you must use his own power against him. He will go around the room shooting different things out at you. He shoots three things. One, if he shoots a blue circle that looks like a necklace at you, just dodge it. When he is at the top-center of the screen go to either the left or the right side of the screen. If he faces you then be ready to deflect. If he is facing straight down he will shoot lightening. Just stay out of the way. The third thing he will shoot is a small glowing ball at you. Use the master sword to deflect it back at him. After a couple hits, he will be history.
He will not admit his defeat, and he will send you to the Dark World. You will be contacted telepathically by Sahasrahla. He will tell you what you need to accomplish here in the Dark World. This is where the actual game really begins in my view.