The Southwestern Sea
Before you head off to find the Ghost ship, a pirate named Jolene attacks. If you try to run, your engine goes dead, so you have no choice but to let her board. You end up in the ship's hold. Walk forward and Jolene enters. When you don't give up Linebeck, she attacks. Avoid all of her attacks by running. When she postures and yells, she's about to unleash a dashing attack that leaves her vulnerable for a second. That's when you attack. When she's taken enough damage, your swords will clash. Rub the stylus against the screen to disarm her. Inspect the large box to find Linebeck. He will give you 5 rupees. From now on, Jolene will occasionally appear on the seas. If she sees you, she'll give chase and inevitably board you again. Linebeck will give you more money each time you beat her until he coughs up 100 rupees. Then, he gives nothing. Head to Spirit Island if you have 10 Power Gems. If you've been following this guide, you do.
Jolene will have accidentally sent you a letter to her sister, Joanne. Turns out Joanne has an odd habit of dressing up as a mermaid. Does that sound familiar? Give this letter to Joanne the next time you go to Bannan Island to receive a Wisdom Gem, as well as a ship part in the mail a day later. Take the letter for now and enter the cave. Open the door and head north to the spring. You will be prompted to offer up one type of Gem. Select Power Gems. If you have 10, the goddess of the spring will power up the Spirit of Power. You can now select this spirit at the collection screen. Since he's been powered up, the Spirit of Power will increase your attack power if he's selected to lead you around. Select him, it'll make future battles much easier. Exit the island and head for Mercay Island.
Go back to that cave on the way to the Temple of the Ocean King that you opened with a bomb. Once inside, jump to the last platform before the chest and shoot the eye on the north wall with an arrow. This extends a bridge to the south, where a River Zora awaits. Kill it and go south to the outside. The tablet outside says that a cliff on this island has a hidden weak spot. To reveal it, you need to shine a beam parallel with a line between the Temple of the Ocean King and Mercay Tavern. Draw a line on your map going from the Temple to the tavern, which is the largest building in the village. Run up the stairs to the right. When you get to the top of the stairs, pull out your bow and shoot the eye on the wall to your left, raising a statue to your right. Run east and south. Open the two chests for a ship part and 100 rupees. Go back to the the statue and hit it with your sword and turn it so its beam points northwest, parallel to the line you just drew. Jump off to the north and follow the beam until you come to the point where the beam hits a cliff. Drop a bomb here and go through the hole that forms. Run straight through the very linear cave until you hit the middle of the bridge. At that point, pull out your boomerang and look to the south. There will be a switch - hit it. If you can't see it, move around on the bridge until you can see it using the boomerang. Open the chest that appears for a Courage Gem. Exit the cave through the exit to the right. Run south and hit the floor switch to extend a bridge to this island. Go to the top of the island to meet Freedle, who will activate the item trading function. If you have any friends with DSs and this game, you can now trade items/ship parts. Run east and south to find a chest with a Wisdom Gem. Now head back to Linebeck's ship and sail to the Northwestern sea on the western side of the rock wall.
Proceed in any direction through the fog. Eventually, the ship's engine will break down. Speak to Linebeck, who will start fixing the motor. The three spirits emerge and agree to help you find the Ghost Ship. The control scheme for the boat will be slightly different now. The Stop and Go toggle still works the same. Now, you will steer by tapping the left and right sides of the screen. The fairies will tell you which direction you need to steer. Ciela will constantly make a beeping noise throughout this part of the game. If you're pointing in the right direction, she'll beep faster. When the fairies start emitting sparklies, you're accurately pointed at the Ghost Ship. Use these clues to navigate the fog. Watch out for explosive barrels littered across the ocean. When you catch up to the Ghost Ship, you'll board.
The Ghost Ship
Head down the only stairs on the level.
Head southwest and jump across the gap to the chest containing treasure. Watch out for the Skulltula that will drop down from the ceiling along the way. Jump back across the gap and head west of the stairs to fight three Wizzrobes. These enemies will disappear and reappear at will. You can only damage them when they've fully materialized. If they're too far away for the sword, try arrows. Avoid their fireball attacks in the meantime. When all three are defeated, flames will recede to the north and west. Go west and find a little girl cowering in fear. She's one of the Cubus sisters, and her other three siblings are locked up by Reaplings in the ship's hold. It's up to you to rescue them. Disregard her suspicious behavior for now and head north. Approach the wall of spikes and use your boomerang to hit the switch to the north. Head east, killing or avoiding the Wizzrobe. Cross the spikes when they retract and hit the switch to the north to deactivate the spikes. Continue east. At the U-bend past the Skulltula, jump south to another platform. Head south and east, killing the Skulltula and rats along the way. Cross the spikes to the north, watching out for the Skulltula in the area between the spikes. Hit the switch to retract some spikes to the north and west. Open the chest for a triangle crystal. Hop back across to the north platform and place the crystal in the pedestal to kill the flames. Go back to the area with the switch and the chest. Go north to find another Cubus sister.
Now you have to get the Cubus sister back to where the first one lies. The annoying thing about the Cubus sisters is that they're deathly afraid of Skulltulas. If they see one, they'll be frozen with fear and won't move until you talk to them after killing the Skulltula. They will also be frozen with fear if you get too far ahead of them. Skulltulas will respawn, too, so you can't kill them too far in advance. Keeping these things in mind, make your way back to the first Cubus sister. Drop off the sister and make your way all the way to the southeast corner of the floor. Go down the stairs.
There are safe areas down here, too. Don't worry, though, as the non-safe areas won't drain your health. These are simply hiding spots from Reaplings. These Reaplings are similar to Phantoms in that they're invincible and you must avoid being seen by them. If they catch you, you'll have to start the floor over. They can move and see through walls, which makes them even more annoying. Head east and a Reapling spawns. Go north past the spikes, then west. Hide out in the safe area. When the Reapling reaches the southeast corner of its patrol and starts to go west, run across the spikes and to the north. When you hit the wall, go straight west. Talk to the next Cubus sister and hit the switch near her, deactivating all spikes on the floor. When you leave the safe area, she'll tell you about two treasure chests to the right. She'll tell you to open the left one. Whatever you do, don't open the left one. This will spawn another Reapling and you will also get a Rupoor, which takes away 10 rupees. Instead, open the right one for a yellow potion, which will restore all hearts when used.
One thing to know about Reaplings - they can hear the Cubus sister's screams. So if a sister gets spooked by a Skulltula, all Reaplings on the floor will rush to your area. If this happens, quickly kill the Skulltula, talk to the sister, and run to the nearest safe area. You will actually use this to your advantage now. Let the sister get spooked by the first Skulltula you see. Kill the Skulltula, talk to the sister, and run back to the safe area where you found the sister. The Reapling will run to your area, see nothing, and leave. Approach the Reapling from behind and shoot its back with an arrow. This will stun it for a few seconds. Run past, killing all Skulltulas that pop up. You want to head for the center of the floor, where a chest containing the round crystal was blocked by spikes. Now that the spikes are retracted, grab the crystal and hoof it to the stairs you used to enter the floor.
Put the round crystal in the pedestal to the north to kill the flames to your left. Head left to the room where the other two Cubus sisters are chilling. Head back down the stairs in the southeast corner.
Make your way to the southwest corner, where there are stairs going down. Unless you accidentally spawned the other Reapling, this should be a breeze.
Kill the Wizzrobe to your right and head right until you reach two signs. Continue past them to the southeast room. 5 Skulltulas lurk in this room. The game helps you out a bit by showing their positions on the map. Slaughter them and head north and west to the smaller of the two safe zones in the middle of the room. Do not hit the switch in the other safe zone, this will spawn a Reapling. Instead, read the tablet, which tells you to pull the levers in the order 24513. So go back to the levers near the beginning of the floor. Counting from the left, pull the fourth, first, fifth, second, and third levers in that order. The order comes from 24513 (41523). This will retract some spikes near the tablet. Go in and lift barrels out of the way until you find a switch on the floor. Watch out for Ropes hidden under some of the barrels. Step on the switch to kill some flames to the left. If you've gone and triggered the Reapling, wait in the safe area with the tablet until the Reapling turns its back to you. Shoot it with an arrow and run past. Go east, north, then west. The chest in the safe area nearby holds 200 rupees. Go to the safe area to the west, where there's a quivering barrel. Lift it up to reveal the last Cubus sister. When you leave, the Cubus sister tells you not to shoot arrows into the Reaplings' backs. In keeping with their habit of giving bad advice, this is actually a good thing to do, as it stuns the Reapling. Go back to the stairs, killing Skulltulas along the way. Go all the way back to B1 - this should be very simple.
Reunite the last sister with her family. This triggers a fight with these sisters, who are actually monsters in disguise. You are teleported to the top of the ship.
Boss Fight: Diabolical Cubus Sisters
You now play a game of "Dead Man's Volley" with the sisters. What this consists of is the sisters throwing energy balls at you and you batting them back with your sword. Three of the sisters will shoot lasers while the fourth shoots the ball. While avoiding the lasers, hit the energy ball back to damage a sister.
Once one sister dies, the remaining sisters will start batting the energy ball back as well. If you miss the ball, it will impact the deck and split into multiple balls that radiate out from the impact point. Occasionally one of the sisters will toss out a fake energy ball that looks like four little balls rotating around each other. Do not hit this, as you can't bat it back.
Once one sister remains, she will shoot out two fake energy balls and one real one. Make sure you hit the real one and prepare for some heavy volleying back and forth. Eventually you will defeat the four sisters.
Use the DS' two screens to your advantage. They both show you what balls are real and show what are not. The top screen is best for this situation, as that it shows which sister will hit the ball. This may not seem like much, but since the sisters hit the ball directly downwards, you might as well pay attention as to who hits it.
Grab the Ghost Key and Heart Container that appear and step through the portal. Make your way down to B2 and open the skull door in the northeast with your Ghost Key. Run up the stairs to find a petrified Tetra. Linebeck and Oshus make an appearance. Oshus reveals that he is the Ocean King, rendered powerless after an attack by Bellum, the game's antagonist. Bellum created the Ghost Ship to drain life force from anyone who entered, drawn by the lure of treasure. Linebeck, crushed by the revelation that there's no treasure on the Ghost Ship, only agrees to help after Oshus bribes him with a wish once his power is restored. Speak to Linebeck in the ship's hold and set sail for Zauz's Island.
Enter the house and speak to Zauz. He tells you that to forge the Phantom Sword necessary to vanquish Bellum, you need the three pure metals Aquanine, Azurine, and Crimsonine. Zauz tells you that in the Temple of the Ocean King, there lies another sea chart. To access this part of the temple, you need to draw the symbol on his wall on the door in B6 where you had to draw the hourglass. The symbol is the Triforce. Head to Mercay Island.
As an aside, there will now be larger pirate ships patrolling the seas, similar to Jolene's ship in size. If you get boarded by one of these and defeat the pirates, Linebeck will give you a Courage Gem. Also, destroying these ships with your cannon will yield a salvage opportunity that disappears once you enter a port.