After solving the wind puzzles on the Isle of Gust, you can enter the Temple of Wind.
Temple of Wind 1F
Go north, then wait for the two gusts of wind to stop, and go north past them. There are three wind gusts above that, but the middle gust is longer than the other two, so make sure to wait for the middle gust to stop before you go north.
North of that, take the bomb and throw it across the gap onto the tile with the explosion picture on it. When the bomb explodes, it will detonate the other bomb flowers, activating both crystals to make two bridges extend to the north. Go north across a bridge.
Go north from there, then east. Push the block in front of the gust of wind, then go east and hit the crystal to stop the second gust of wind. Go east and up the stairs.
Go south across the bridge, and go down the stairs at the end. Go south and touch the door with the circles on it, then go south and step on the switch to create a shortcut to the exit.
From there, go east and up the stairs, then continue going east, running past the gusts when they stop. Run east to jump over the gaps, then go down the stairs at the end and go north to the room above.
Kill all the Ropes that appear in this room, then go west to a room full of rupees. Go west and push the block to reach another room full of Ropes. Kill the ropes and go north, but ignore the wind gusts up above.
Go west and you find another statue blowing a gust of air. You can pull and push this statue, so pull it onto the tiles in the ground with the explosion symbols on them. Then stand in that gust of air and run to the left to be pushed over the gap.
Step on the switch to create a shortcut, then go down the stairs.
Temple of Wind B1
The map shows some hidden monsters in this room. Throw a bomb at each of the rocks indicated by skulls on the map, then throw another bomb at the Rock Chuchu that appears. Then you can hit the chuchu with your sword to kill it. Kill all three to unlock the door.
Go southeast, then up the stairs, then east. There are miniblins in this area, as well as a switch that opens a door in the southwest of the area. Step on the switch and go up the stairs that were behind that door.
First, go east to find a chest behind two pots.
Then go west and up those stairs again. Go north and fall down into the lower area with the checkered floor. Go to the top and stand on the upper gust of air to float up to the chest on the ledge up above.
Go south again and up the stairs, then fall into the lower area. Move the block to make it cover the third gust from the bottom, then stand in the second gust from the bottom and you will land on the block. Go east from there to drop down to a new area. From there, go east and south, and down the stairs.
Temple of Wind B2
Use a bomb flower to bomb the crack in the wall. There are sandworms in the area above, so stay on the paths in the sand. Go to the area northwest of where you entered this room. There is a platform in the center with a map on it. Copy the Xs onto your map, then go around the room using the shovel to dig up the holes where you marked your map.
Each time you dig a correct hole, a torch lights up in part of the room.
In the west side of the room, there is a treasure chest. There is a cracked wall north of that, but without bombs, you can't do anything about it.
After you dig up the correct holes, go to the door in the north wall that opened. In the next room, bomb the cracked blocks, then go up the stairs. Go south across the bridge, then push the wind statue to the left to make the windmill spin.
Then go back to the sandworm room. Go to the southwest corner and go up the stairs.
Go east and up the stairs, then cross the bridge to the east and pull the statue to make the windmill spin. Get the key that falls.
Go to the southeast corner of the room and stand on an air vent to be pushed onto the block that you pushed earlier. Then go east and go down the southeast stairs.
In the sandworm room, go north and open the locked door there, then go north and open the chest to get bombs.
Go to the north wall. There is a hidden cave to the left of the door in the north wall. Put a bomb between the third and fourth columns from the right. The cave behind the wall contains a big green rupee.
Then go to the northwest corner of the sandworm room and bomb the wall to reach a new area.
Put a bomb on the air vent, then after the cracked block blows up, stand on the air vent to go up to the ledge. Then go up the stairs.
Put a bomb on the air vent here, and it will start a chain reaction that opens the door to the east. When the door opens, go through it quickly, because it only stays open for a limited time. To the east, put a bomb on the checkered tile in the floor. This will open a secret hole. Go north through the hole, then east and south. Tap the door with the circles on it to open it, then go south and go up the stairs.
Temple of Wind 1F, part 2
Put a bomb in front of the north wall, at the fourth square from the left. Then go north, west, and south. Put two bombs, side-by-side, on the tiles that have explosion icons on them. This will activate both crystals at once, opening the door to the south.
Go south and open the chest to get the boss key.
Go to the left and fall down the ledge, then put down the boss key and use a bomb on the air vents to break the cracked blocks up above. Then take the Boss Key and stand on an air vent, then tap the barrier to throw the Boss Key into it to unlock it. Then go north and through the door.
Go north. A wind will blow from the north. When you reach the top of the area, stand on the vents to go up. Check on the sign to make a blue warp point appear. Then go north up the stairs.
Cyclok, Stirrer of Winds
There are three spots in the floor that randomly create stationary cyclones. When Cyclok is hovering over one of those cyclones, throw a bomb into the cyclone to make the bomb fly up and hit Cyclok. It will fall to the ground, where you should hit him with your sword until he gets back up.
Cyclok can come down to the ground and charge toward you, and he will send down small cyclones that will hurt you if they touch you.
Keep an eye on Cyclok's shadow so you will know which cyclone to throw a bomb into in order to hit Cyclok. Cyclok moves more quickly as the battle progresses.
After you defeat Cyclok, you get more sand for the Phantom Hourglass, so it has a maximum time of 12:00 minutes.
Neri, the Spirit of Wisdom, joins you.
Open the chest to get a Heart Container, then step into the blue warp point in the middle of the area to leave the temple.