The Ghost Ship
After boarding the Ghost Ship, Linebeck will comment on how scary it is, and Ciela will taunt Linebeck by calling him a "cucco". Anyway, we need to get on with rescuing Tetra, so in the first room that we are in, head to the door on the left.
The first sister
Basement 1: Continue heading left until you get into a closed door battle with some Poes, who will constantly appear and reappear and attack you with weak unblockable fireballs. Just get close enough to them to strike them when they appear. When that battle's over, the closed door will reopen, and a wall of fire to the north and to the west will disappear. Go to the room on the left where you'll find a girl in an orange cloak, who will tell you she's the youngest daughter of the house of Cubus, and that her other three sisters are on this boat waiting to be saved. Agree to help rescue them, and she will warn you about the Reaplings on board the ship.
The second sister
Now head right and then up and then right until your path is blocked by spikes. Slay the Skulltula that drops down on you first, then direct your Boomerang to switch orb that's north of you to disarm the spikes. Then go to the right, avoiding the rotating wall of fire, and go around the snaking path to the right, hitting another switch orb with the Boomerang to disable more spikes. More of this path will be blocked by a wall of fire. Instead, jump across the gaps and then head south and to the right, slaying rats and Skulltulas along the way, then go north past the moving spikes and hit the switch orb to disable some spikes in a door as well as some to the left of you. Go to the treasure chest that's to the left of the door, and in it you'll find a triangle crystal that you need to put in a pedestal. Bring it close to the wall of fire and then throw it across the gap to the left of you. Then jump across the gap and carry it to the pedestal to place it there. The wall of fire will now go out.
Now go into the room near where you found the treasure chest, and you'll see a girl in a blue cloak. She is one of the older sisters, and she needs you to escort her to her youngest sister. Lead her back along the same way you came, but make sure you're not jumping across any gaps while doing so, because she will not jump across any gaps. While you are escorting her, she will cower in fright whenever a Skulltula drops down near her. Slay the Skulltula, and then tap on her to get her to continue following you.
The third sister
When the two sisters meet, they will gush over each other, being happy to see each other again, but the youngest sister will tell Link that the older sister has not seen Tetra either. We now need to rescue the other two sisters. Head in the same direction as you were when you were rescuing the second sister, but after crossing the gaps head to the staircase to the south and go down into Basement 2.
Basement 2: When we enter the floor, we will see a Reapling appear in the same way that a Phantom Guardian did in the Temple of the Ocean King. Reaplings behave similarily to the Phantoms in that they cannot be killed and that they patrol the floors in the same manner. However, Reaplings can now pass through walls, which Phantoms cannot do. Fortunately, there are also Safe Zones here and the next floor down which we can hide in to protect ourselves from Reaplings the same way we do the Phantoms. Another fortunate is that we can stun the Reaplings by shooting them in the back with an arrow.
From where we enter this floor, go to the right, then up, left, up, and then all the way to the left while watching the Reapling's movements. Depending on where the Reapling finds you, head for the nearest Safe Zone. At the northwestern corner of this floor, go down and then left where you'll find a girl in a yellow cloak, who is one of the other older sisters. Hit the switch orb in that Safe Zone, and the spikes blocking your way to the Safe Zone immediately to the right of you will be disarmed. The girl will tell you there's a treasure hidden in the left treasure chest in that Safe Zone. However, open the right treasure chest, and you'll get the Yellow Potion that will restore all your hearts.
Now retrace your steps on this floor and on Basement 1 to bring her to her other two sisters. On Basement 2, there's a shortcut you can take in the center that has a treasure chest. In it you'll find the round crystal. Take it with you to Basement 1 and put it on a pedestal to remove the wall of fire so you can bring her back faster.
The fourth sister
The three sisters will gush over each other, being happy to see each other again, but the youngest sister will tell Link that this sister also has not seen Tetra. We now need to rescue the last older sister. Head in the same direction as you were when you were rescuing the third sister, but when you enter Basement 2, head to the left and go along the snaking path to the staircase that leads to Basement 3.
Basement 3: From where you enter this floor, go to the right, where you'll see five pull switches that we need to pull in the right order. Continue to the right, and you'll enter a closed-door battle with some Skulltulas. Slay them, and the closed door will reopen, and the wall of fire blocking our way to the north will disappear. Now go up and take your first left into the Safe Zone to hit a switch orb to remove spikes blocking the south door of a room full of steel drums. At the same time, though, this will cause a Reapling to appear. Watching the movement patterns of the Reapling, go up, then all the way to the left until you enter the Safe Zone. In there is a stone tablet that gives you a numbered code on how to use the pull switches: 24513. Translated, from left to right, it means second, fourth, fifth, first, and third. Go back to the room where the pull switches are and pull them in the order shown in the code. This will remove the spikes on the north door of the steel drum room. Now go back and enter the room from the north (don't enter from the south, or you'll fall through a trap door!). Inside the room, clear away the drums on the left side until you see a floor button. Step on it, and this will cause a wall of fire to the left of this room to disappear. Now we need to travel all the way to the north, then all the way to the left, and then down, left, and up until we are in the Safe Zone with some steel drums, one of which is rattling. Pick up that steel drum, and we find a girl in a green cloak who is the oldest sister. Escort her through the same floors that we went through until she is reunited with the three other sisters.
Ghost Ship Boss: Diabolical Cubus Sisters
Once you bring all four sisters together...guess what? They reveal their actual intentions with Link, and now take him to a place where they will play Dead Man's Volley with him. All four of them turn hideous and will float high in the air above Link.
As the battle starts off, three of the sisters will fire deadly beams down to the ground while the fourth sister hurls an energy bolt at Link. Watch the appearance of the bolt: if it's a single-part bolt, you strike it with the sword so it goes back to the sister who hurled it; if it's a four-part bolt, avoid it because it will not bounce back but rather split into smaller bolts.
When the first sister is eliminated, two of the remaining sisters will fire the beams while the third hurls an energy bolt. However, after Link deflects the single-part bolt back, it will bounce among the other sisters until it is deflected back to the ground, usually faster. Get quickly to where it will land and knock it back upward, or else it will either dissipate or strike Link.
When the second sister is eliminated, one of the remaining sisters will fire a beam while the other hurls an energy bolt. Again, they will bounce the deflected bolt among themselves for a bit before sending it back down. Repeat the same strategy as you did earlier.
When the third sister is eliminated, the remaining one will hurl two four-part bolts and one single-part bolt in three directions. Get to where the single-part bolt is headed and strike it back toward her. Here it becomes more like Dead Man's Pong as you will have to watch for where the energy bolt will be deflected to.
When the last sister is eliminated, she will give you the Ghost Key. You will also get a treasure chest that contains your next Heart Container, and a blue portal will appear that will take you back to Basement 1 of the Ghost Ship. Head for Basement 2 and then go right and then up to a skull-faced door that we can unlock with this key. Enter the room and go up the stairs and we will find...Tetra?