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NOTE: This Walkthrough will cover, each and every Heart Piece, Item, Boss, and everything else.
You now have two pendents, and only need one more. Before getting the last pendent there is a few items that can be picked up. From where you are after defeating the Desert Palace head all the way down and then exit to the right. Continue going right to the next screen. Go right a bit and enter the building here. Once you are inside, push the two blocks on the side up and then the middle one to the right or left and open the chest for some bombs.
Exit, and then re-enter. This time move the middle block up and either one of the others block to the right or left and then head up to the next screen. You can kill the anti-fairy if you would like. Pull the switch that is located at the top-right and you will see water go through the passage.
Leave the building and a heart container will be waiting for you just to the left of the building. Now head right one screen, up two screens, right a screen, accross the bridge and up two screens, continue going up on the right side of the river. Head right a screen, and go all the way to the right.
Now that you have the Power Glove you can list the large boulder. Lift it up and then head a screen to the right. Kill the Buzzblob if you wish. Then dash into the rocks and go up a screen on the right side this time. Kill the enemies and then head up a screen.
You are now at Zoras Waterfall. Follow the path of water all the way to the top, then take a right. The path then splits off, just stay along the bottom path and it will lead link to King Zora. Talk to him and purchase the flippers for a 500 rupees. With the flippers, Link can now swim in the water.
Once Link gets the flippers head directly South. Swim down the first waterfall and then follow the path of shallow water. It will turn left and go into a forest area. Keep following it until you find a Quarter Heart Container. Grab it and then head back to the water and jump down one of the waterfalls here.
Back on the path, head left and then down and out of Zoras Waterfall. In this screen head all the way to the left and the top. You will ses a waterfall. Swim into it to discover a secret area. It will ask if you would like to throw an item into the pond. Throw in your boomerang and let the magic begin. When the fairy asks if you threw it in, say yes. Since Link was honest, the fairy will give Link a Magic Boomerang, which travels a full screen length.
Exit the pond and re-enter. Now throw in your sheild this time. Say that you threw it in, and because you are honest, the fairy will give you an upgraded sheild. This sheild can deflect more attacks.
If you have an empty bottle with you, leave the pond and re-enter and throw in a bottle. The fairy will give Link the bottle back, but it will be filled the Green Potion. Green Potion restores Links magic meter. Exit the waterfall. Go straight down and you will see a tornado thing in the water. One of the tornados dont move and are part of the Zora Waterways system. It will transfer link to some part of Hyrule. Swim into it to be transferred to Lake Hylia.
Once you have gone through the waterway you will be in the center of Laky Hylia. Swim to the up and you will see an island. Swim to the right of the island and head up. There is a ladder here. Dont go up the ladder but follow the river just to the left of the ladder and head up a screen. Continue following the right right a screen. Now swim under the bridge. Go up the ladder here and talk to the man under the bridge, and he will give Link a bottle.
Swim back right two screens. Then down a screen. Now head up the ladder, and up a screen. Head left a screen and up two screens. Head left across the bridge and up a screen on the left side. From here head left three screens. On this screen, go up a bit and then go right a screen using the top passage. Run into the rock and open up the chest to get a quarter heart container. Exit the cave and head left a screen. Head up a screen.
On this screen head up a bit and you will see a cave that is being blocked by a boulder. Lift the boulder and then head into the cave.
Once inside the cave jump down and onto the path, take the first possible right. The path will split into two, take the bottom route. Go all the way to the right until you hit a wall and there is a tiny passage just above. Go up a bit and then go right. There is an old man standing here. Talk to him and he will follow you.
Head right to the next room. Keep heading right. Just go around the holes. Go all the way right. The man will tell you to take a right. So do so and head down. Follow the path out of the cave. You are now on Death Mountain. Head down and right until you reach a door. The man will no longer need your help, and since you helped him he will give Link the Magic Mirror. You can go into the cave and talk to the man to fill up your hearts if you need to.
From just outside the cave head right a bit and up the ladder. Head right a bit and then head back left on the upper part. Go all the way to the left here. There is a long ladder here, climb up it. Stay against the southern wall here. You will see an area where you can jump down, and under it is a cave. Dont jump down this one but go a bit further and you will see a cave under you and a place where you can jump down, do so and enter into that cave.
Go up the stairs to the next floor. Then just go down and you will see the heart container. Get it and then fall down the hole. There are fairies to the right if you need them. Otherwise head left a screen and then down and out of this cave. Jump down and then head back left again. Go up the long stairs and then head all the way right. You will see a heart container here but it cannot be reached at the current moment. Head right and walk into the portal that is there.
You are now in the Dark World, but since you do not have the Moon Pearl yet, you are a bunny.
Head left a bit. You will see two animal looking things walking around. They obviously didn't have the moon pearl so they changed to animals. Head left and use the mirror where Link is standing in the picture to the right.
Once you are back in the Light World, head right and pick-up the heart container here. Head up and jump off the rock to the top.
Head right a bit and you will see the Tower of Hera. Head up and enter.