After landing, Skipper shows you where his perched shack is and asks you to go fetch his sea chart. Cross the pier, take a look at the Bird Statue, go right and get rid of the Electro Spume with a bomb. Dash to the platform to the right, clear out another Electro Spume, then shoot the Clawshots at the target to the top right, climb and attack the two Deku Babas. Take a look at the flying enemy (Peahat), grab it with your Clawshots, then aim at the target to the left and climb! Get rid of the yellow Chuchu, then place a bomb in front of the cracked wall on the right.
Get in this new passage while being careful not to be hit by Chuchus, then shoot the Clawshots at the "Peahat", then at the next target, at another Peahat and at the target in front of you, and climb. Get on the bridge and you will see a Moblin with an Iron Shield. Dash to it to jump over it ^^ then get rid of the Quadrobaba and open the small chest to get 20 rupees.
Go right, aim at the target with your Clawshots, climb, then go left. Take a look at the kind of flower and ask Fi what it is to learn that it's a Peahat, a kind of plant that can fly if you pull off the flower at its top with your Whip. Get rid of the nearby Furnix first, then use your Whip at the Peahat, let it fly a few meters above you, then use your Clawshots at it, then at the target to the left. Climb and get to the summit of this peak. Look northeast, a Deku Baba is hidden next to the target! Send the Beetle at it and cut the stem when it gets out! Then use your Clawshots at the target, then at another one behind you and climb. Get rid of the two Furnix, then shoot the Clawshots at the Peahat when it's high in the sky, then at the other Peahat, then at the target in front of you and climb. Open the Skipper's house door.
Get rid of the Arachas, then vacuum the sand with the Gust Bellows. Open the chest to find the Ancient Sea Chart, then read the messages on the walls. Get out, go right, grab the handle and slide down to the Moblin! then go to the other mechanism and slide down to the pier. (You can also go to the diving platform and do a free jump towards the blue chest down to the south, which contains 100 rupees!) Talk to the captain which now wants to get his ship and shows you the position of the Shipyard on the map. Add another mark at this location, then sail carefully to this place while avoiding rocks, red barrels and enemies! Land at...
Skipper tells you that long ago this place was a city with inhabitants, then shows you the main building of the Shipyard. He advises you to use the cart network to find the back door of this building. Cross the pier and take a look at the Bird Statue to the left. Climb the stairs, go right, fight or avoid the Lizalfos, then climb the next stairs and get into the mine-cart station. Talk to the Goron Gortram who strongly advises you to read all the instructions concerning how to use the carts. Read the four panels hanged on the left wall and get into the cart: Yipee yai yay! Incline your Wiimote to keep the cart straight on the tracks and hit the brakes when it's going too fast! Get off at the northeast station.
Go ahead, climb the stairs, go ahead, get rid of the Arachas, then turn right. Before getting into another cart, read your map carefully to know where you have to go next. Get into the cart, then upon reaching the first intersection, go right, upon the second one, to the right, then jump to cross the gap, go left, right, then left to follow an easier way to the Terminus Station! Save using the Bird Statue, then open the door to the Construction Bay. Jump into the "sandbox" ^^, then use the Gust Bellows in the middle of the area to free some black pieces of metal... oh no! It's just another Moldarach! Fight off this scorpion like you did with the Mining Facility one, then Fi tells you that there is probably nothing else to find there. Leave this building using the closest door, then get back to the robot. (If you don't have much hearts left, get back to the first station and sit next to the Goron.) Talk to Skipper which will inform you that your next destination is the Pirate Stronghold! After putting a new mark on the designated position, sail to this stronghold while avoiding rocks, barrels and enemies to land foot on...
After the captain's cheering, go across the pier and take a look at the Bird statue. Climb the steps, look up and launch the Beetle in one of the "nostrils" of the beast to pick up three silver rupees! Now go right and open the door next to the crates. Take a look at the map so you can see the size of this place! then after taking note of Fi's advice, go northwest according to the map and open the door. Vacuum the sand to get a red rupee, then go ahead to fight two Lizalfos (and pick up two Lizalfos' Tails). Get into the next room, get rid of the Electro Spume with a bomb, dash to cross the sand, then open the next door.
Climb the steps to the left and Fi will show you the Timeshift Orb, designed to be carried around. Pick up the Timeshift Orb, go left and follow the corridor up to the Technoblins room. Drop the Orb, attack the two Technoblins, then pick the Orb again and go on. Drop it to destroy the Beamos, then pick it up again and go left. Drop the Orb to this place, backtrack, go left towards the chest and pick up 100 rupees! Take the orb back, go down the path, pick up an Ancient Flower to the left, then keep on walking along the wall to climb a slope. Jump (still while holding the Orb) on the pillar in front of you, then to the right, in front, left, in front, left and towards the passage.
Go ahead, drop the Orb in front of the bars, go left, grab and lower the lever, then pick up the Orb and go ahead to the main room. Walk along the wall to the right, then when the wall goes up, take two or three steps back, drop the Timeshift Orb and dash towards the chest to find a common treasure. Pick up the Timeshift Orb again, attack or avoid the Deku Babas, go towards the opposite corner of the room and fight off the Deku Babas and Technoblin in the corridor.
In the next room, get rid of all the enemies, then drop the Timeshift Orb between the two entrances leading to the corner of the room which has a switch. Get there from the south, pull/push the crate on the switch, which will lower the bars in front of the door, then pick up the Orb again and go west. Go a little further, drop the Orb next to the passage to the left, then go opposite (to where you came from). Open the blue chest to get a Monster Horn, use your Gust Bellows on a sand pile to get two red rupees and notice the lever behind the barbed wire. Pick up the Orb again, throw it further and get rid of the two Beamos. Drop the Orb behind the barbed wire, where the Beamos were. Get back to the other side of the room and grab and lower the lever to lower the bars to the right. Take the Orb back and drop it so one of the two Armos (not the two of them) comes back to life. Destroy it and do the same with the second one. Pick up the Orb, go south and put it down on the pedestal in the first room.
The huge stone jaw will open and a door will now be accessible. Leave the stronghold using this newly appeared door and go straight ahead. Fi tells you that the masts and sails have to be from the ship you are looking for and adds the ship to your dowsing system. Go back to the small robot and once more get back on the sea.
On board, Skipper says that his invisible boat will appear upon receiving damage. Use your dowsing to find that the ship is east of here, then sail southeast, then east and use your dowsing function regularly to follow the ship which is actually moving! When the dowsing is blinking really fast, speed up the boat to try to bump into the invisible ship. If you made it, quickly fire one or two cannonballs at it, then use the dowsing again and go after it to bump and attack it several times. Then the ship will become visible...