Go right, get rid of the Keeses and open the door to the left. Get rid of the Electro Spume to the right by rolling a bomb at it, then cross the sand by dashing. Go to the end of the corridor and open the door.
Go into the corridor while getting rid of the Arachas, take a look at the Bird Statue at the back, then Fi shows you the door leading to the boss. Follow another corridor while being careful with the Keeses, then open the door. Notice the door with the crystals, then vacuum the sand with your Gust Bellows to discover four rudders drawings. Look at the two rudders around the door: the red part is at the top. On the ground, facing the door, the rudder with a red handle (so it's the first one) points at the bottom, then next to it, the rudder with two red handles points at the top, the rudder with three red handles points at the bottom, and the rudder with four red handles points at the right. Go the door and hit the crystals following this sequence: down, top, down, right. Open the now unlocked door and pick up the Small Key in the chest. Get out, go back to the first underground level, then to the main floor and save using the Bird Statue.
Mini-boss: LD-002G Scervo - Pirate Robot
Unlock the door and a skeleton dashes at you! Ask Fi about its name and to understand that this is the android that stole the ship. Run to it, raise your shield when it's about to strike and quickly hit it with thrusting moves and some jumping attacks to make it draw back. Once it's at the end of the plank, it will resume its attacks against you. Dash again towards it and attack it so it draws back, then upon reaching the end of the plank, it will lose its sword and strike back. Keep on fighting it until it falls over, which will make a chest appear. Open it to find the Bow! along with a 20 arrows quiver. Go back inside, sit next to the statue to refill your hearts, then get out using the door in front of you. Take a look at the blue eye-like mechanism on the mast. Shoot an arrow at the "eye" so a Timeshift Stone appears, then draw your Bow as much as you can and shoot an arrow at the Timeshift Stone after zooming. The boat comes back to life!
Look up again and get rid of the Bokoblins with your arrows, then climb at the top of the mast using the big ladder. Fight off the green Archer Bokoblins, go right, then shoot an arrow at the blue eye on the left. Grab the handling to go up, then get rid of the Bokoblins and go to the other side. Shoot another arrow at the other blue eye, grab the handling and go up once again. Attack the Bokoblin, then get next to the mechanism, stick your sword into it, rotate it a quarter turn to the right and push it: The door leading to the inside of the boat is now free of access, along with the Timeshift Stone.
At this time, Skipper will congratulate you and ask you to free its crewmates, then he shows you their location. Shoot an arrow at the eye to the right, grab the handling to go down, then jump on the back deck and destroy the barrels to the right to capture a fairy in an empty bottle. Use your Clawshots at the target on the mast, then on the target behind you and again at the target lower behind you and let go. Open the chest to get a Piece of Heart! then go to the other side (south) and play your Harp next to the butterflies: a Goddess Wall! Go back up using the Clawshots and get back to the door leading to the inside of the ship to go down to the...
Go right and open the door to the left. Get rid of the Technoblins, then go to the small room to the left and get rid of another Technoblin after Fi has shown you the Timeshift Stone outside. Break the barrels to pick up arrows and use your Bow to reach the Timeshift Stone. Then you can go right and open the chest to get a Map! Grab and lower the lever to create a shortcut, get back left, shoot another arrow at the Timeshift Stone, then follow the corridor in front of you and go down the stairs to the...
Go ahead, destroy the Beamos, then open the next door leading to the prisoners' brig. Fight the two Technoblins, then talk to the small robot behind the bars. It tells you that the engine room is under this cell, that the power has first to be turned back on, and it shows you the location of the two power generators on the first basement. Go back to the deck, shoot an arrow at the Timeshift Stone, get back inside and go to the...
Go back right, open the door, follow the corridor to the right and stop next to the rusty fan. Shoot an arrow at the eye on the back wall which will unlock the door to the left. Open this door, then get on the crate to the right and push it as much as possible to free another fan. Then stand on the switch and shoot an arrow at the eye ahead through the fan! The next door will now be unlocked. Leave this room and get back on the deck.
Shoot an arrow at the Timeshift Stone, then go back down to the first basement and get back to the same corridor. Open the first door to the right and get rid of the Technoblin. Then, thrust your sword into the generator, turn it to the left and push it. The Engine Room is now working, but you have to switch the second generator on. Leave this room, go right and open the door to the left. Attack the two Technoblins, then push the crate at the back of the room onto the switch on the ground: Two windows will open and allow you to reach the ladder leading to the third basement. Get back once more to the deck.
Climb the ladder on the left or on the right, then shoot an arrow at the Timeshift Stone. Then, go right (north on map) and shoot an arrow at the eye over the safety boat: the latter goes down one level. Jump on the safety boat and get in the...
... through the window. Get into the room to the right, then grab and lower the lever which will unlock the door to the left. Break the barrels if you need more arrows, then stand into the light and shoot an arrow at the Timeshift Stone to bring the boat back to life. Thrust your sword into the generator, turn it to the left and push it: The Engine Room is now fully operational. Get out from the door, go left and open the door to the left. Climb on the ledge of the left window and go down the ladder.
Get in through the window, follow the corridor and open the door. Walk carefully under the three cubes, then climb the ladder. Use the Whip at the hook, then turn around towards the ladder to the right, swing (while climbing on the rope a little) and jump ahead. Climb the ladder, then open the five chests to get two Monster Horns, one Evil Crystal and two silver rupees! Go back down and jump to the right. Dash through all the cubes in one run, then climb the ladder. There use the Whip on the hook again, climb a little, then swing and jump on the cube. Jump on the following one, then jump ahead. Grab and lower the lever to create a shortcut, then get in the small passage and climb the ladder at the end.
Grab and lower the lever to lower the bars and free Skipper's crewmates. The small robot tells you that the control room is next to this room, but you need a special key that you can find inside the captain's cabin, and it gives you a Small Key! Get back to the third basement following the same path (using the shortcut), climb back to the first basement using the ladder outside and get back on the deck.
Climb the ladder to the right, go straight ahead and unlock the door. Go down the stairs to notice that you are now blocked, then get back on the deck, shoot an arrow at the Timeshift Stone, then go back to the cabin and go back down. Notice the Bird Statue, then go left. Get rid of the Arachas, then shoot an arrow at the Timeshift Stone through the wire fence on the ceiling, attack the Technoblin and destroy the Beamos. Stand on the switch which creates an opening, then shoot an arrow at the eye at the back of the room through the opening: The door on your side will unlock. Open this door, then quickly attack the Beamos, then the one on the left and finally the one behind! Get in the cage and open the chest withholding the Squid Carving! Get back on the deck, then inside the main part of the boat and go back down to the...
Get to the Bird Statue, save, then take a look at the great door and place the Squid Carving inside the lock. (The small wave must remain visible and the red circle must point at the southwest.) As soon as you get in, tentacles break through the ground! Since you can't do anything, get out and get back to the corridor. Two other tentacles break in! Fi suggests you get back on the deck. Perform the Skyward Strike on the tentacles to cut them, then go ahead and climb the stairs while the ship is sinking! Avoid the barrels, cut two other tentacles, climb the stairs, then open the door to the deck.
Boss: Tentalus - Abyssal Leviathan
While tentacles are rising everywhere through the deck, raise your sword to the sky until it's loaded and always keep moving, then perform the Skyward Strike while inclining your sword a bit towards a tentacle to cut it. After cutting off three other tentacles, Tentalus will get out of the water! Draw your Bow and shoot at its unique eye to hit it. When it's falling down, run to it, aim at its eye and strike it as much as you can. Repeat these steps twice more and try to pick up some hearts and arrows during the fight. If you ever get caught by a tentacle, shake the Wiimote and the Nunchuck to free yourself.
The second phase begins when it starts to attack the boat that will sink even more. While avoiding the barrels, run to the crate, climb on it and on the upper deck. Keep on shooting arrows at its red eye, then run and slash it as much as possible. Then it will throw its "hairs" at you that will try to bite you! Cut them with your sword, grab some hearts, then shoot another arrow at its eye as soon as it stops attacking you! When the arrow reaches its target, run, strike the eye as much as you can, and the boss will be defeated once and for all.
Pick up the Heart Container, then aim at the Goddess's symbol and perform the Skyward Strike. Nayru's blue flame will come out and storm into your sword that will get longer and more resistant. From now on, Fi can detect more elements at the same time through the Dowse function. Another triangle appears on your right hand and Fi informs you that you are ready to learn a new song at the Isle of Songs.
Back to the Sand Sea, Skipper tells you that it will fix its ship with his crewmates' help.