After collecting all of the Tears of Nayru in Nayru's Silent Realm, you receive the clawshots and can access the Lanayru Sand Sea.
Reach the Pier
Use the clawshots to go west along the columns. Once you are hanging from a target, you can use the clawshots again on another target. If you don't have the targeting option while hanging from a clawshot, press B.
After reaching the main port area, go to the north and climb up the boxes, then use the clawshot to go to the blocked-off area. You will find a Goddess Cube in the cave.
Help the Skipper
Go to the end of the pier and hit the timeshift stone on the boat. Talk to the robot. He is the skipper of the ship that protects Nayru's Flame, but some pirates came to take the flame and he ended up in this port with this small boat. The skipper says that the ship protecting the flame has probably been turned invisible. Agree to help him find the ship.
He says to start by going to Skipper's Retreat to get the Sea Chart there. He marks the Skipper's Retreat on your map with an X. You can move the boat with the control stick, speed up by holding the A button, ready the cannon by pressing B, and fire the cannon by pressing A.
Go to the X marked on the map and stop the boat next to the pier, then press A to get out.
The skipper's shack is at the very top.
After walking to the end of the pier, turn right and kill the Electro Spumes with bombs, then make your way across. Use the clawshot on the peahat up ahead to get up onto the ledge. Bomb the cracked wall to find a tunnel. Go through and use the peahats and wall targets to reach the top of the spire.
Wait for the Iron Shield Moblin to rotate its shield and set it down, then press A to run up the shield and get behind him. Kill the quadro babas in this area. Then use the clawshot on the vines on the spire behind the chest containing 20 rupees. The vines take you to a Goddess Cube. Press B while on the vines to take out the clawshot.
Go back to the platform where you got the 20 rupees. Use the clawshot on the target just past where the furnix is flying. Pull the furnixes toward you by whipping their tails, then use a fatal blow to kill them.
Use the whip on the inactive peahat to make it start flying. Use the clawshot on it to ride over to the target. Clawshot the target to get up onto the pillar.
The next clawshot target is blocked by a deku baba, so use the beetle to cut it down. Then use the target and get on top of the next pillar. Kill the furnixes, then clawshot the peahat nearby. Wait until you can see the peahat on the other side of the rock and clawshot over to it. Then use the target on the pillar where you find the Skipper's Shack. There are Sand Cicadas that you can catch here if you wish.
Go inside. Use the gale bellows to blow away all of the sand. Open up the chest to get the Ancient Sea Chart.
Go outside. You can skydive off of the pier on this pillar to get the blue chest that you saw below. Tilt the remote to make yourself land on the platform with the blue chest. Use the sailcloth to avoid getting hurt when you land. The chest contains a silver rupee.
If you don't want to try to get the silver rupee, grab the red bars to slide down to the bottom level.
Talk to the skipper and he will mark the Shipyard on your map. Sail toward it. You will encounter enemies on the way. Press B to get the cannon ready, then aim by pointing with the Wii Remote, then press A to shoot.
Go next to the shipyard pier and press B to put away the cannon, then press A to get onto the pier. The skipper will say that you need to go into the Mine Cart Station and ride a mine cart to the back door of the Shipyard.
Go up the stairs past the bird statue, then go to the right and fight the two Lizalfos. The key is to watch them to make sure they aren't about to attack, and get out of the way if they are.
After killing the Lizalfos, go up the stairs and go into the mine cart station. Talk to the goron, then read the signs on the wall to learn how to use the mine cart.
Mine Cart Ride
Go up to the mine cart and press A to get in. Tilt the Wii Remote to balance the cart when you go around curves. Press B to slow down. Shake the remote upward to jump over obstacles.
You don't lose hearts if you fall off, so don't panic here.
When you approach a curve, lean toward the inside of the curve. In other words, if the track is curving to the left, lean left. If the track is curving to the right, lean right.
The first cart ride doesn't include any obstacles or jumps, so just practice leaning before curves.
After this cart ride, you end up in a small room. You can catch some gerudo dragonflies up ahead. In the building up ahead, watch out for the arachas that drop from the ceiling.
If you keep going straight, you find a bar that you can grab onto to slide back to the beginning if you want more practice.
Otherwise, from the building, take the side path to find another mine cart. The sign says "to construction bay" and there is an inactive robot here.
During this cart ride, there will be places where the track splits. You need to lean in the direction that you want to switch to. You have to do this in order to get out of the loop that you first end up in. Lean to the right to get out of the loop.
There are some wooden barriers with red Xs on them that you need to lean away from to avoid crashing into them. You might want to press B to slow down, because otherwise you have to be very quick to notice the barriers before you crash into them. There are also some jumps in the track that you will crash at if you are not going quickly enough, so be sure to flick the remote upward to jump over these gaps.
Once you reach the end of the track, you end up at the construction bay.
Fi says to blow the sand away to look for a clue to the ship's whereabouts. However, when you blow away the lump in the middle, a Moldarach pops out.
As before, you need to slash the eyes in the claws in the proper direction so you don't hit the pincers. After you hit them enough times, the claws will come off. If Moldarach burrows into the sand, blow the sand away with the gust bellows until it pops out again. Thrust the sword at Moldarach's eye to hurt it. If you run away when Moldarach's eye turns red, you will never get a chance to attack, so stay close and keep doing thrust attacks even if Moldarach's eye turns red.
After the fight, Fi realizes that the construction bay has turned into a monster nest and probably doesn't have any clues. Go back to the robot skipper and he will say to go to the pirate stronghold. Get into the ship and he will mark the stronghold on your map. Sail to it.
You can't get into the giant teeth here. Don't go too close to these teeth or you will sink into the sinksand around them.
Send your beetle into the nose of the mouth to get three silver rupees.
Go to the right of the teeth on the lower platform and you will find a door. Go inside.
Go through the unlocked door in the northwest side of the room.
Kill the two lizalfos up ahead. Throw a bomb at the electro spume in the quicksand to kill it. Stay close to the edge of the wall and run over the floor pieces to avoid sinking into the sand.
In the next room, you will find a Timeshift Orb. Pick it up. You can't go back the way that you came. Instead, just follow the straightforward path ahead. The orb will remove the spiky barrier, so just walk through.
Up ahead, you will revive some technoblins. If you are careful, you can place the Timeshift Orb such that you only revive one technoblin at a time and can fight them individually.
There is a beamos up ahead. Be careful to avoid its gaze, and quickly slash it horizontally twice to break its segments, then thrust at the eye to destroy it.
There is a blue chest ahead, but don't bring the timeshift orb close to it, because doing so will activate an electric barrier that blocks it. Set down the orb and walk to the blue chest, then go back to the orb.
In the room up ahead, when you walk around with the timeshift orb, the sand will disappear and some platforms will rise when you get close. Go down the ramp on the side of the room and get the Ancient Flower that appears, then go up the other ramp in the room. You can jump onto one of the platforms that appeared, then while carrying the orb you can jump your way across to the door.
Up ahead, leave the orb on the floor so you can go through without activating the electric barrier. Then pull down the red bar to lift the bars and go back to get the orb.
In the next area, deku babas will appear around the room, so go slowly. If you bring the orb close to the blue chest, two platforms will rise up and block it. Set down the orb and then run across the sand between you and the blue chest to open it. Then run back over the sand and get the orb. Go slowly to avoid getting too close to the deku babas. A wall appears in front of the exit, and you will have to kill a deku baba to safely walk around this wall and reach the exit.
In the tunnel ahead, three babas will appear. If you are careful about where you put the Timeshift Orb, you should be able to revive and fight them one at a time.
Continue to the end of the tunnel and make your way slowly to fight technoblins and babas one at a time. Be sure to kill the present-day Electro Spumes that disappear when the Timeshift Orb is brought near.
In this room, there is a small room with a box and a switch. One of the doors will be covered with bars when you press the switch, and the other door will be blocked with an electric barrier if you bring the orb close to it. You need to be able to walk to the orb after putting the box onto the switch, so make sure that the orb is close enough to the electric barrier door that you won't need to run over the sand to get the orb, but leave it far enough away that you won't activate the electric barrier. Push the box onto the switch, then walk to the orb and go through the door that you just removed the bars from.
In the next room, set the orb down and open the blue chest. Move the orb so that you can destroy the nearest beamos without activating the other one. Once you destroy this beamos, put the orb where the beamos was. This should remove the barrier from the red bar switch in the other room without activating the second beamos. Go around to the red bar and pull it down. Go to the orb and run back to the large room. You should be able to run out of the way of the second beamos without getting zapped.
Bring the timeshift orb close to one of the statues near the exit so that you only activate one of them. Defeat this armos statue the way that you did before: use the gust bellows on the rotating part on its head, break the purple crystal, and repeat. Do the same for the other armos statue to open the bars. Go through.
Put the orb onto the pedestal. The teeth of the pirate hideout will open. Exit through the door that just opened.
Find the Ship
Walk to the bridge and Fi will add the ability to dowse for the ship that protects Nayru's Flame. The ship is somewhere in the sea to the east.
Talk to the robot skipper and get into the boat. He will say that the ship is invisible but if you attack it, it will show itself. You can dowse while on the ship, so once you get past the spumes that attack you, start dowsing and press A to accelerate toward the dowsing signal. You might bump into the ship. This doesn't hurt you. Just aim your cannon and shoot at the invisible ship. After you hit it a few times, it will become visible and Link will climb onto the Sandship.