After you collect 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 press the indicated button to use the Clawshots again on another target.

After you reach the main port area, go to the north and climb up the boxes, then look to the west and use the Clawshot to go to the blocked-off area. You will find a Goddess Cube in the cave, as well as a large number of Arachas that fall from the ceiling. It unlocks the chest in the Bazaar of Skyloft at Gondo's Scrap Shop, which contains a Gold Rupee, worth 300 rupees.

Help the Skipper

Go to the end of the pier to the west and hit the crystal on the boat. Talk to the robot. This is the Skipper. Agree to help him find the ship that protects Nayru's Flame.

Start by going to Skipper's Retreat to get the Sea Chart there. The robot marks the Skipper's Retreat on your map with an X. Press the indicated buttons to move the ship, speed up, ready the cannon, and fire the cannon.

Go to the X marked on the map and move the boat next to the pier, then press the indicated button to get out.

Skipper's Retreat

Your destination is the skipper's shack, which is at the very top.

After you walk to the end of the pier, save at the Bird Statue. Then follow the path and use the Beetle to drop bombs on the Electro Spumes, or kill them with Skyward Strikes, then make your way across. Use the Clawshots to go up onto the columns, and when there aren't any more Clawshot targets within reach, use the Clawshots on the Peahat that is floating nearby. From there, use the Clawshots to reach the next target. Kill the Yellow Chuchu that appears near the cracked wall, then bomb the cracked wall to find a tunnel. Go through, kill the Yellow Chuchus that fall from the ceiling, and use the two 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 run up the shield and get behind him. Or you can stun it with the Slingshot and hit it with your sword until it recovers, then run away and stun it again, and so on until you kill it. Then kill the Quadro Baba up ahead and open the nearby chest to get 20 rupees. Then look southwest to see vines on the stone column. Use the Clawshots on the vines to reach the Goddess Cube on the far column. It unlocks a chest northwest of Fun Fun Island that contains a Potion Medal.

Use the Clawshots on the vines to go back to the column that you were on. If you want to return to the sky now, you can go to the zip line and press the indicated button to grab it and go back down to the Bird Statue.

Back at the top of the zip line, use the Clawshot on the target just past where the Furnix is flying. Pull the Furnix toward you by whipping its tail when it lowers it, then draw your sword, and use a fatal blow.

Use the whip on the inactive Peahat nearby to make it start flying. Use the Clawshots on it to ride over to the target. Use the Clawshots on the target to climb onto the column.

The next Clawshot target is blocked by a Deku Baba, so use the beetle to cut it down. Then use the Clawshot target and get on top of the next column. 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 column where you find the Skipper's Shack. There are Sand Cicadas on top of the building that you can catch here if you wish.

Go inside. There are some Arachas hiding in the sand. Use the Gust Bellows to blow away all of the sand, revealing rupees, Amber Relics, and a chest. Open up the chest to get the Ancient Sea Chart.

Go outside. You can skydive off of the pier on this column to reach the blue chest that you saw below. Use the Sailcloth to avoid getting hurt when you land. The chest contains a Silver Rupee, worth 100 rupees. From there, you can use the Clawshots to return to the area with the boat. You can use Skyward Strikes to kill the Electro Spumes in the way.

If you don't want to try to get the Silver Rupee, you can walk to the zip line west of the Skipper's Shack to slide down to the bottom level.

Shipyard

Talk to the skipper and he will mark the Shipyard on your map. Sail toward it. You will encounter enemies on the way. Follow the on-screen instructions to get the cannon ready, aim, and shoot.

Move the boat next to the shipyard pier, put away the cannon, and press the indicated button to get out.

Go up the stairs past the Bird Statue, then go to the right and fight the two Lizalfos. Afterward, go up the stairs and go into the Mine Cart Station. Talk to Gortram the Goron, then read the signs on the wall to learn how to use the mine cart. You can sit on the stool to recover hearts if needed.

Mine Cart Ride

Go up to the mine cart and press the indicated button to get in. Follow the on-screen instructions to balance the cart, slow down, and jump over obstacles.

You don't lose hearts if you fall off, so don't panic.

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 may find 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 zip line that you can use to slide back to the beginning if you want more practice.

Otherwise, from the building, take the west path to find another mine cart. The sign says "to construction bay" and there is an inactive robot here.

You can check the map to see the layout of the track up ahead.

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 start 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 slow down beforehand, 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 lean into every curve to go quickly enough jump over these gaps.

Once you reach the end of the track, you end up at the construction bay.

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.

Moldarach 2

As before, you need to slash the eyes in the claws in the proper direction so you don't hit the pincers. If an eye in a claw turns red, run a safe distance away to avoid its attack. 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 central 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. But if it covers up its eye, and the eye turns red while covered up, run to a safe distance to avoid its tail attack.

After the fight, 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.

Pirate Stronghold

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 nostrils above the teeth to get three Silver Rupees.

There is a door around the east side of the lower level, but beware of the Yellow Chuchus that appear along the way. Go through the door.

Go through the unlocked door in the northwest side of the room.

Kill the two Lizalfos up ahead. Farther 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 to get the Silver Rupee, worth 100 rupees, 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 if any Ancient Flowers appear, collect them, then go up the ramp on the west side of the room. While carrying the orb, you can jump onto one of the platforms that appeared, then jump to the other side of the platform. Make your way from platform to platform to reach the north door.

Up ahead, leave the orb on the floor so you can go through without activating the electric barrier. Go to the other side of the bars and pull down the red bar to lift the bars. Go back to the orb and take it through where you opened the bars.

In the next area, Deku Babas will appear around the room as you proceed, 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 and get a random treasure item. Then run back over the sand and get the orb. A wall appears in front of the exit when you approach. 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. The present-day Electro Spumes will disappear with the Timeshift Orb is brought near. You can place a bomb where they will reappear, then move the Timeshift Orb away so the bomb explodes on them as soon as they reappear.

In this room, there is a small room with a box and a switch. This switch only stays pressed if you push the box onto it. 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. So place the orb just out of range of the electric barrier so that you can walk through that opening without sinking into the sand. 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 go west to open the blue chest and get a random treasure item. Then slowly take the orb south so that you can destroy the nearest Beamos without activating the other one. Once you destroy the corner Beamos, put the orb where it 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 back to the orb and bring it through the door that you just unbarred. You should be able to run out of the way of the second Beamos quickly enough to avoid getting zapped.

Bring the Timeshift Orb close to one of the Armos statues near the exit so that you only activate one of them. Use the Gust Bellows on its head to open its mouth, and break the two crystals, using a forward thrust to break the one that is blocked on the sides. 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 Stronghold will open. Exit through the door that just opened.

Find the Ship

Before you proceed, turn around and face the door that you came out of. Use the Clawshots on the target, then use the Clawshots again on a target farther up. Climb up and you find a Goddess Cube. It unlocks a chest on a floating island in eastern Skyloft that contains a Piece of Heart.

From the Goddess Cube, go back to the stronghold entrance, then go toward the Skipper's ship. Fi will add the ability to dowse for the ship that protects Nayru's Flame. The invisible ship is somewhere in the sea to the east.

Run across the narrow strip of sinksand on your way to the skipper and the boat.

Talk to the 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 deal with the Spumes that attack you, start dowsing and press the indicated button 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 you will climb onto the Sandship.