After you activate the generator in the desert, you gain access to the Lanayru Mining Facility.
Get a Key
After you enter, you can save at the Bird Statue nearby. There are small spiders on the floor called Arachas. If they latch onto you, follow the on-screen instructions to shake them off.
Use the Beetle to pick up the bomb on the column and drop it on the Electro Spumes on the north side of the room. Then use the Beetle to drop a bomb into the basket of the northwest statue. (The other statues hide Arachas and a blue rupee.)
By running, you should be able to just barely make it to the northeast platform, 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 northwest platform if you run. Go up the wall to pull down the red bar, to unlock the north door. Run back across the sand and go through that 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, which indicates that it will attack.
After you kill the two Staldras, you can't go through the east or west doors right now, so instead go to the northwest, where there are several boxes. Push a box against the platform so you can climb onto it, run up the wall, and reach the north door. Go through.
Save at the nearby Bird Statue if you wish, then look east to see two wooden crates at the base of a ladder. Use the Beetle to take a bomb and blow up those crates. Go toward the ladder, killing the Yellow Chuchu that attacks. Then run across the gap and climb up the ladder. Kill the Thunder Keese that attack, then open the chest to get a key. The nearby ladder is blocked at the top, and the other paths in this room are blocked, so just go back to the previous room.
Get the Gust Bellows
Use the key on the locked door 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. You can use the Hook Beetle to knock into it and make it explode. Go east until you reach an inactive conveyor belt going south. Go south along it and kill the Froak and the Arachas on the vines, then climb the vines.
Look to the west, toward the door that you entered through, and you will see a column above the door with a bomb on it. Use the Beetle to take a bomb and drop it onto the wooden crate at the top of the ladder in the southwest corner of the room. Climb the ladder and step on the switch. This removes the bars from a 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.
Make your way east, killing Beamos and running to get past the rapid conveyor belts in the way. Climb up the ladder in the southeast of the room and run up the wall to pull down the red bar, which removes 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 you reach the other side, go west and 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 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.
There are square platforms throughout the room. Make the Froaks float into the piles of rock by hitting them with the Slingshot. (They will only explode if you hit them with the Slingshot when they are not spiky.) Then go up the ladder in the southeast corner of the room and jump northwest over the square platforms, but be aware that the Froaks in this room will reappear a short time after they explode.
There is a blue chest in the northwest corner of the room that contains a random treasure.
Climb up onto the north platform, then jump to the platform on the west side of the room and push the box off of the edge to give yourself a shortcut. Then go to the platform on the north side of the room and climb up the ladder. Kill the Arachas that fall from the ceiling, then open the chest to get 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, climb the ladder, and blow the sand away to go through the door.
Push the box to the side to move it out of the way of the ladder. Then go down the ladder and go through the south door.
Go to the northeast corner of the room and kill the Arachas, then blow away the sand around the metal box, and blow the other piles of sand away to reveal a switch. Push the box onto the switch. This opens the locked west door. 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. Make your way from platform to platform, until you reach the southeast platform, which has a big pile of sand on it. Blow the big pile of sand away to reveal a crystal. Activate it.
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.
Jump onto the nearby platform and use the Gust Bellows to move it west. Then go north and use the Gust Bellows to move the northern platform close to you. Jump onto it and use the Gust Bellows to move the platform so you can reach the blue chest on the nearby platform. It contains a Monster Horn.
Get back on the movable platform, and move it south again. Go to the bars in the wall, and use the Gust Bellows on the pinweel (also known as a propeller) above the bars, until the bars open all the way (if you stop before they open all the way, they won't 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 or swing your sword 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 or sword swing to knock the missile back at the Sentrobe, killing it. Sentrobes drop many rupees when they die, but in this area, most of them will probably fall into the pit.
There is a movable platform on the west side of the room. Use the Gust Bellows to make it move to the ledge where you can jump across to it. Stand on it and move it to the west side of the room and jump across to the other side. Climb the ladder and kill the Beamos. Then use the Gust Bellows on the pinwheel on the wall to raise the bars all the way, then go through the door.
Kill the two Staldras, then blow the sand off of the metal box, blow away the pile of sand in its path, and move the metal box to the far end of its path. Use it to reach the top of the wall above. Use the Gust Bellows to blow the Arachas off of the ledges on the west side of the room, and blow the sand off of the Amber Relic in the corner. Then go back to the north ledge. Blow through the bars to get rid of the sand that hides a crystal. 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 you destroy the first crystal, run away and then repeat the process, using the Gust 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 east door.
Step on the nearby blue switch to raise the bars.
Roll bombs at the Electro Spumes to get rid of them from a distance.
There is a narrow safe path submerged in the sand. Use the map to see it and walk along it. When the path is going west, blow away the sand against the west wall to find a small tunnel. Crawl through it, using the map to help you see where to go. At the end, beware of the Arachas on the ceiling. Blow away the sand to find an Amber Relic. Open the chest to get a random treasure.
Go back to the big sand room and use the hidden sand paths to reach the ledge to the north. Blow away the sand to find an Amber Relic, and possibly a blue rupee (not guaranteed to be there).
Then go south from there and go to the other pile of sand against the west wall. Blow it away to find another hidden passage behind the sand in the west wall. 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 Gust 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. If you need to bring it back to the start, pull down the red bar near its starting point. 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 or sword swings 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 to allow the mine cart to continue.
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 east side of the room and blow away the sand. Ignore the nearby ladder for now; a metal crate is blocking it. Go to the side of the mine cart and hit the crystal with a forward thrust to activate it. Follow the mine cart and hide behind it as necessary 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.
Run up the wall to pull the red bar and make the cart go to the end of its path. Then stab the crystal inside with a couple of forward thrusts to deactivate and then reactivate it, making it go in the other direction. Before the Beamos is reactivated, run into the area behind it that you unlocked when you raised the bars earlier. Go through the door.
Go across the conveyor belt, wait for the air to stop blowing across your path, and make the Arachas fall off of the vines. There are shadows on the vines that show where the air vents will blow. Make your way to the right, avoiding the air vents, then climb up when the air stops blowing.
Kill the Thunder Keese and look at the south wall. 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 crystal. Activate it.
Jump back across the platforms and kill the Beamos, then go north and run up the wall to pull the red bar down, making the movable platform come over to you. Use the platform to go all the way west, then kill the Sentrobe. Bomb the basket platforms to reveal the pattern 2-3-1.
Blow air at the other movable platform to move it south to where you can reach it. Jump onto it and move it north. Move the crate to the side so that you can reach the ladder.
If you need bombs, hit the nearby barrels. Then get onto the eastern platform and move it south, and throw a bomb into each of the three statues' baskets. They can be knocked down in any order. 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. (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 you kill the Armos Statues, go through the bars to open the chest and receive the Ancient Circuit. Go back the way you came and go down the ladder, and kill the Beamos that is going back and forth. Then go to the conveyor belt and carefully run west along it, avoiding the air vent and the rocks while picking up Stamina fruit. Go through the door at the end.
Reach the Boss Door
Look south and go up the nearby ladder. Go to the end of the path, killing Thunder Keese along the way, to find a chest that contains 20 rupees. Then go to the nearby metal crate and pull it to unblock the ladder.
Then go to the northeast corner of the room and save at the Bird Statue if you wish.
Activate the crystal in the mine cart with a forward thrust into the side. Then you have to stand on the movable 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, you can pull down the red bar to make the mine cart reach the end of the path, which removes the barrier from in front of the boss door. 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 the indicated button 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. If an eye turns red, run away to avoid getting hit. If you get caught in the pincers, follow the on-screen instructions 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. You will need to wait for it to turn red and quickly stab it before Moldarach attacks. Run away 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 Gust Bellows to blow the sand away and make Moldarach pop out. If you are not quick enough, it may try to hit you with its stinger from under the sand. If Moldarach closes its eye, run away avoid it when it charges forward. Watch out for Arachas that may appear during the battle.
Otherwise, keep 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 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 cutscene, you will know that your next destination is the Sealed Grounds.
You can use the Beetle to get the rupees from the columns in this area, and use the Gust Bellows to blow away the sand and get an Amber Relic, rupees, and Lanayru Ants.
Go east and save at the Bird Statue. You can use the Gust Bellows on the sand piles to the south to find rupees and another Amber Relic. Then go talk to Gorko if you wish. Then use the Bird Statue to go back to the Sky, where you can prepare before returning to the Sealed Grounds.