Save at the save point to the left. The spiders on the floor are called arachas. They are very easy to kill, although if you are not quick, they will jump on you and you will need to shake the nunchuck and remote to get them off of you.
Get a Key
Use the beetle to catch the bomb on the pillar and kill the Electro Spumes on the far side of the room. Then use the beetle to drop bombs into the baskets of the statues.
By running, you should be able to just barely make it to the platform on the right, where you can run up the wall and pull down the red bar. This opens the bars to a chest that contains a red rupee.
You should also be able to just barely make it to the platform on the left if you run. Go up the wall to pull down the red bar to unlock the door in the middle that goes to the next room. Run back across the sand and go through the door.
There are two Staldras in here. Kill them by waiting for the heads to be in a line, then slash in the direction of all three heads to hit all of them at the same time. Be ready to use a shield bash if the monster's eyes turn red, because it will attack.
After killing the two staldras, you can't go through the left or right door right now, so instead go north and push one of the boxes on the left side to the north platform so you can stand on it and run up. You can stand on the box by walking toward it until you climb up. Go through the door.
Go to the right and use the beetle to bomb the crates at the foot of the ladder across the way. Then run across the gap and go up the ladder. Kill the keese that attack, then open the chest to get a key. Go back to the last room.
Get the Gust Bellows
Use the key on the locked door on the left from where you came in. It's on the east side of the room.
A Froak is nearby. It floats around, and when it gets close to you, it becomes spiky. Froaks will explode when they touch a large solid object like the wall, or you. Use the sword to knock them into a wall and make them explode.
Go up to the arachas on the vines up ahead to make them fall off, then kill them. Climb the vines and use your beetle to get a bomb from the pillar above the door that you entered the room through. Drop it onto the wooden crate at the top of the ladder. Climb the ladder and step on the switch. This removes the bars from a time crystal, but if you walk off of the switch, the bars go back up, so use the beetle to activate the crystal.
There are beamos around the room now. To defeat them, slash their bodies in the direction of the blue line to destroy each segment, then stab the eye with a forward thrust when the eye is on your level.
There is a conveyor belt in the middle of the room that moves very quickly. Don't try running up the conveyor belt yet. Instead, go across it and climb the ladder across the way. Run up the wall to pull the red bar down, removing the bars from the door on the other side of the room.
Then go back down and run up the conveyor belt. Be sure to sidestep the lumps of stone that get it your way, and pick up the green fruits so you don't run out of stamina. After getting to the other side, go up the ladder and get the 20 rupees from the chest.
Then go up the stairs on the east side of the room and run up the conveyor belt here to find a red bar switch near a tall beamos. Cut the beamos's segments by slashing in the direction of the blue line, then stab the eye with a forward thrust. Run up the wall to pull the red bar switch and unlock the door. Go through.
In this room, there are square platforms throughout the room. Make the froaks float into the piles of rock by hitting them with the slingshot. Then jump over the square platforms. There is a blue chest in the northwest corner of the room that contains a gold skull. Then go up onto the platform on the west side of the room and push the box off of the edge to give yourself a shortcut. Go to the platform on the north side of the room to receive the Gust Bellows.
Get the Map
Use the Gust Bellows to blow the froaks away from you. Now you can use the gust bellows to blow away the piles of sand that you have seen all over the place. Just be careful because some of the sand piles have arachas hidden inside. Go to the platform on the west side of the room and blow the sand away to go through the door on the west side.
Push the box down to give yourself a shortcut to this area.
Now go back to the second room of the dungeon, where you fought the two staldras. Blow away the sand around the metal box in the northeast corner, and blow the other piles of sand away to reveal a switch. Push the box onto the switch. This opens the locked door on the left. Go through.
In this sandy area, make your way across by running to the nearby platforms, avoiding froaks and arachas on the way. You will reach some bars that you can't open. Run to the far platform in the corner that has a big pile of sand on it. You should be able to just barely make it to this platform. Blow the big pile of sand away to reveal a timeshift crystal. Hit the crystal to send this room into the past.
There are platforms with blue and red magnet-shaped weather vanes on top. If you blow one side, it makes the platform move one way. If you blow the other side, it makes the platform move the other way.
Go back across to the bars that you couldn't open. Before going through, use the middle platform to go over to the blue chest, which contains a monster horn.
Go back to the bars. There is a pinwheel on top, also known as a propeller. Blow the pinwheel with the gust bellows until the bars open all the way. Then you can stop blowing air at it and the bars will stay open. There is a beamos rolling back and forth in this area. You can kill it by cutting its segments in the direction of the blue line, then stabbing its eye with a forward thrust. Or you can just run behind it and wait for it to go past the ladder. Climb down the ladder.
There is a sentrobe nearby. To kill it, use a shield bash when it shoots a missile at you. After the missile hits it, the sentrobe will send out two sentrobe bombs. You can kill them by cutting them in the direction of the blue line on their bodies. After that, you can use another shield bash to knock the missile back at the sentrobe, killing it. Sentrobes spit out a bunch of rupees when they die, but they will all probably fall into the pit this time.
Use the bellows to make the lower moving platform come to you. Then stand on it and move it to the end of the room and jump across to the other side. Climb the ladder and kill the beamos as before. Then use the bellows on the pinwheel on the wall to raise the bars all the way, then go through the door.
Kill the two staldras in here, then blow the sand off of the metal box and push it to the far end of its path. Use it to reach the top of the wall above. Use the bellows to blow the arachas off of the ledges on the side and blow the sand off of the amber relic in the corner. Then go back to the ledge with the bars. Blow through the bars to get rid of the sand that hides a timeshift stone. Use the slingshot to activate it.
There is now an armos statue next to the door. Go into the circular area around it to make it come to life. Back away while holding the gust bellows. Blow air at the weather vane switch on the statue's head to reveal two purple crystals. One of the crystals can only be destroyed with a forward thrust, and the other just needs to be hit with the sword in any direction. After destroying the first crystal, run away and then repeat the process, using the bellows to reveal the second crystal so you can destroy it with the sword.
Once you kill the statue, the bars will be raised and you can go up and open the chest. It contains the dungeon map.
Get the Ancient Circuit
Go through the door that the armos statue was blocking.
The sand on the far left hides a blue switch. Step on it to permanently raise the bars to the middle area.
There is a narrow safe path submerged in the sand. Use the map to see it and walk along it. There is a narrow passage hidden behind the sand to the left. Crawl through, using the map to help you see where to go. The chest at the end contains a blue bird feather.
Go back to the big sand room and use the hidden sand paths to reach another hidden passage behind the sand in the wall to the north. Use the map to see which way to crawl through the passage, then go into the new room. Drop down to the floor.
Blow the sand away from the floor to find a safe path through the spikes. There is a switch on the west side of the room and a chest in the northwest corner that contains a red rupee. Press the switch to remove the bars from the door. Go through that door.
Use the bellows to blow the sand away from the mine cart. Then you can activate it by standing on the side and doing a forward thrust with your sword. You can't get rid of the pile of rock on top.
The cart will automatically move. Follow it, standing on the platforms that appear. When the cart reaches the bars, it stays there. The sentrobe is activated, so use shield bashes to hit the missiles back at it, and when the sentrobe bombs float down, kill them by slashing in the direction of the blue line on their bodies.
After the sentrobe is gone, use the pinwheel to open the bars all the way.
Walk along the platforms that appear. Walk on the side of the cart opposite from the beamos so that the beam hits the mine cart instead of you. There is a beamos up ahead that blocks the mine cart. Kill it by slashing the segments in the direction of the blue line, then stab the eye with a forward thrust.
Up ahead, stay on the other side of the mine cart to avoid the two beamos, then go across the platforms and run up the wall to pull the switch, causing the mine cart to come to the end of the path. Open the door by blowing air at the pinwheel.
Save at the bird statue, then go back through the bars that you opened. Go to the right side of the room and blow away the sand. Activate the mine cart like you did with the other one, stabbing it in the side with a forward thrust. Then move along with the mine cart and hide behind the cart to avoid the beamos. When the cart goes near the pinwheel, quickly blow air at it to raise the bars back where the beamos was.
Once the mine cart reaches the end, stab the crystal inside with a couple of forward thrusts to deactivate and then reactivate it, making it go in the other direction. Run into the room that you unlocked behind the beamos. Try running across to that ledge before the beamos is reactivated. Go through the door.
Go across the conveyor belt and make the arachas fall off of the vines. There are shadows on the vines that show where the air blows. Go to the right side, staying under the shadows, then climb up when the air stops blowing.
Kill the keese and go to the right. There are some statues on the wall holding baskets, so throw a bomb into each basket. Go to the pile of sand on the other side and blow it away to find a timeshift crystal. Activate it.
Go to the other end of this ledge and run up the wall to pull the red bar down, making the moving platform come over to you. Use the platform to go across, then kill the sentrobe. Bomb down the basket platforms to reveal the pattern 2-3-1.
Blow air at the other moving platform to move it close to you and jump on. Go across. Move the block to the side so that you can reach the ladder. Then roll the platform on the side of the room and knock down the basket platforms with a bomb. Don't worry about which order to knock them down. Each one has a switch behind it. You need to hit the switches in the right order, BUT the order is mirrored from what was shown on the other wall. So the first one to hit is on the LEFT, the second one to hit is on the RIGHT, and the final one is in the middle. Basically, each number on the opposite wall refers to the switch directly across from it, which is why it's mirrored.
When you do it correctly, the bars open. Go through and defeat the two armos statues, staying away from the middle in order to prevent both statues from coming to life at the same time. Kill them the way you did the other one: blow air at the spinning switch on its head to reveal the purple crystals, then hit the crystal with the sword, using a forward thrust to break the crystal inside of the mouth.
After killing the armos statues, go through the bars to open the chest and receive the Ancient Circuit. The bars will be removed from a door. You can reach it by carefully running on the conveyor belt.
Reach the Boss Door
Use the bird statue that is up the stairs. Then go up the ladders to the left of the door that you came through to find some treasures and healing items. At the end of the ledge, push the block down to create a shortcut.
Go back to the area with the bird statue. Activate the time crystal in the mine cart with a forward thrust into the side. Then you have to stand on the wind platform and blow it across slowly while making sure that the mine cart is next to you, blocking the gusts of air that blow out of the wall.
Once you make it across, use the Ancient Circuit to unlock the door. Rotate it so that the shape matches the slot in the door. The door will glow when the Ancient Circuit is positioned properly. Press A to put the Ancient Circuit into the lock and go through the door.
First, you have to destroy the claws. To do this, hit the eyes in the claws by slashing in the direction that isn't blocked by the pincers. So if the pincers are horizontal, do a vertical slash to hit the eye, and so on. If an eye turns red, just run away to avoid getting hit. If you get caught in the pincers, shake the nunchuck and remote to escape.
After hitting the pincer eyes enough times, the claws will be destroyed.
Now you have to do a forward thrust into the main eye. Run away if the eye turns red or if the stinger is about to stab you. If Moldarach disappears under the sand, look to see where the sand is moving, then use the bellows to blow the sand away and make Moldarach pop out. Then continue doing forward thrusts at the main eye until Moldarach dies.
Reach the Temple of Time
After the heart container appears, the sand will drain out of this room and you will end up at the bottom. Get the heart container and go through the door.
You need to activate a timeshift crystal to go down this big hallway, but there isn't one nearby. Look at the ceiling in the middle of the long hallway and you will see the crystal. Use the beetle to activate it, then jump into the mine cart. Go through the door on the other side to reach the Temple of Time.
After the cut scene, you will know that your next destination is the Sealed Grounds. Talk to the goron and then use the bird statue to go back to the sky. Fly to the green column of light and dive down.