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After making some preparations, you can go to the Temple of Time and open the Door of Time.
In the Temple of Time, step onto the red rug in front of the altar and play the Song of Time. Go through the Door of Time and walk up to the Master Sword. If you did everything in Before the Temple of Time, you will only need to put the Master Sword back twice.
When you are ready, take the Master Sword. Watch the cut scene that follows.
Go to the Graveyard in Kakariko Village. Walk to the graves along the left wall. Pull back the grave that has flowers in front of it and drop into the hole.
Inside, walk forward and Dampé will challenge you to a race. He will drop flames along the path that will hurt you and stop you briefly if you hit them, so watch out. If you are careful, you can use the flames to follow Dampé's path. None of the correct paths have rupees on them, so if you are on a path with rupees, you have gone the wrong way.
When you reach the room where Dampé stops, he gives you a chest containing the Hookshot. Take it, then exit. Play the Song of Time next to the blue block to get out.
You end up in the windmill on a ledge. Carefully jump over to the piece of heart to collect it.
Go down to the floor of the windmill and take out your ocarina when standing near the angry-looking man. He will teach you the Song of Storms.
If you want to learn a warp song that takes you instantly to Lake Hylia, read the Ice Cavern section to find out how to learn the warp song. You should get the hookshot before attempting the Ice Cavern.
Go to Lake Hylia and go to the Lakeside Laboratory. If you planted a Magic Bean here, you can ride to the roof to get a piece of heart.
If you have Zora's Tunic and the Iron Boots, (check the Ice Cavern section to find out how to get these), go into the Lakeside Laboratory and sink to the bottom of the water in here. Roll attack the crate to find a gold skulltula. Use the hookshot to kill it.
Go back outside and talk to the scarecrow in Lake Hylia. If you taught the scarecrows a song before getting the Master Sword, then this scarecrow will say that his friend Pierre will appear in certain places if you play Scarecrow's Song.
Now that Pierre will appear, you can go fishing again. Walk near the platform with the door to the fishing pond. Navi will fly over and glow green. When she does this, it means that you can play Scarecrow's Song and Pierre will appear. You can use your hookshot to pull yourself up to him. Play Scarecrow's Song. If it doesn't work, try moving around and playing it from a different spot. Go up to the fishing pond and pay to fish. Just like in the past, the biggest fish is hanging around the logs near the center of the pond, so try to catch it there. Once you get it, have the guy weigh your fish and you win the Golden Scale, which lets you dive even deeper than the Silver Scale.
Go to Kokiri Forest. At night, you can find a gold skulltula on the back of the house next to Saria's House. On one of the two pillars on the roof, there is a gold skulltula at night.
Go to the Lost Woods. Go right, left, and right. Mido will be there blocking your way. Play Saria's Song for him and he'll move out of your way. Go through the hole he was blocking.
Go left after passing through the hole that Mido was blocking. In this area, if you planted a magic bean in the past, ride the bean sprout up to the top area where there is a gold skulltula at night.
From the hole that Mido was blocking, go straight, left, and right.
There are moblins patrolling the maze up ahead. If you taught the scarecrows the song, you can make Pierre appear and avoid the Moblins below. At the entrance to the maze, Navi will float up to a ledge and turn green. Play Scarecrow's Song to make Pierre appear. You might want to kill the Moblin in the corridor to keep it from attacking you while you try to get up. Hookshot up to the ledge, then, if it's night, jump to the platform where you can see a gold skulltula, and kill it with the hookshot and get the token.
If you didn't teach the scarecrows the song, go toward the opening in the wall across the way, but don't go into the long passage yet. Instead, use Z-Targeting or press C-up to look both ways. You'll see a moblin patrolling the passage. Hit it with the hookshot to kill it. Whenever the passage turns a corner, look down the path with Z-targeting or C-up and kill any moblins in the passage. Go the same way that you went to learn Saria's Song earlier in the game. Before going up the stairs at the end, turn around and go up the ladder here. If it's night, jump to the platform where you can see a gold skulltula hanging out, and kill it with the hookshot and get the token.
Now go back to the stairs going up. To get rid of the huge moblin, zigzag down the path to avoid the shockwave that the moblin creates with the giant club. Get behind the moblin and slash its legs until it dies. Go up the stairs. Sheik arrives and Then teaches you the Minuet of Forest. This is a warp song. Use a warp song anywhere to be transported to the matching grey Triforce pedestal in the ground. You have seen one here and one in the Temple of Time. If you went through the Biggoron's Sword side-quest you learned another warp song from Sheik.
After Sheik leaves, use the hookshot on the tree branch hanging above the broken stairs to get up. Go through the door to enter the Forest Temple.