Phantom Hourglass Walkthrough – Ghost Ship

After completing the Temple of Courage, return to Linebeck and you’ll find that Oshus is also at the shore. Ciela will combine with the fairy and awaken as the Spirit of Courage. With all three fairies awakened, they are now able to help Link find the Ghost Ship.

Back on the ship, set a course northward and you’ll immediately be interrupted. A pirate by the name of Jolene will appear and ambush your ship. Linebeck will hide away and Jolene will confront you, eventually starting a battle.

Just keep on aggressively swiping at Jolene. Once she jumps back, she will wind up for a strong attack. When she does this, side step the attack and then deliver a sword slash of your own. Repeat this process until you have hit Jolene three times. At this point you will need to rub the stylus left and right when it is prompted on the screen. Do so quickly to defeat Jolene and she will leave. Confront Linebeck who is hiding in the box and he will reward you with a blue rupee.

From this point onward, Jolene will always appear on your sea chart and if you sail close to her, she will ambush you. While this can be a tad bit annoying, it will help you rack up some rupees as Linebeck will reward you with a red rupee and then a big green rupee for the second and third times you face off with her.

At this point you can sail directly to the fog in the northwest quadrant to look for the Ghost Ship. However, there are a number of optional quest items to collect. Follow along to get these optional goodies, or jump to the next section of this chapter to continue onward in the main quest.

Optional: Jolene's Letter

Return to Molida Island and you should have a special delivery in the mail from Jolene. It turns out the message is actually for Joanne, Jolene’s sister. If you recall, Joanne is the mermaid girl that we found at Bannan Island earlier in the quest. (Note, if you have never encountered Joanne, you won’t get this letter at this time.) The postman will ask you to deliver it to Joanne, so agree to do so.

Optional: Quiver Upgrade

Don’t leave Molida Island just yet, as there are more goodies to collect here. Run over to the Molida Island shop and you’ll find new items available for sale. In particular, the merchant is now selling a Quiver, available for 1000 rupees. If you’ve been following along, you should be close to 1,000 rupees by now. If so, go ahead and purchase the quiver, which allows you to carry up to 30 arrows. If you don’t have the money, you can buy this at anytime at the Molida Island or Mercay Island shops.

Optional: Romanos' Shooting Gallery

Make your way to the east end of the island and enter Romanos’ hut. He has just opened a shooting range that you can now play with your bow. It costs 20 rupees to play, so go ahead and pay the price.

You have 70 seconds to play and you have an unlimited amount of arrows. The ghosts will give you 10 points each, and if you hit ghosts consecutively without wasting an arrow, you’ll get an additional 10 point bonus, all the way up to 50 points. Do not shoot the girl targets, otherwise you will lose 50 points. There are a variety of rewards, depending on your score.

0 – 1299 Points: Nothing 1300 – 1699 Points: Random Treasure 1700 – 1999 Points: Quiver Upgrade, and then a Ship Part 2000 Points or More: Heart Container, and then a Ship Part

Before leaving Molida Island, make sure you check out the mailbox, in which you likely have acquired a letter from Romanos. He once again thanks you, and to celebrate the grand opening of his new mini-game, he will give Link a ship part.

Optional: Spirit Island Upgrade

Return to Linebeck to set sail. If you’ve been following along with the guide, you should have acquired 10 Power Gems by now. If so, set sail southward from Molida Island to the previously uncharted Spirit Island.

Walk inside to reach the Spirit Shrine. Select the Power Gems, and this will upgrade Leaf, the Spirit of Power. Link’s sword will now burn flames. Be sure to go into the Menu and select Leaf so that you can reap the benefits. Now Leaf will stay out instead of Ciela.

Optional: Treasure Map #10

Return to Mercay Island and make your way back to just outside of Oshus’ house at the western side of the island. If you recall, a statue near the Temple of Courage hinted to a lost treasure. Just south of the tree next to the cave by Oshus’ house, pull out the shovel and dig up a Treasure Map.

Optional: Mercay Island Cave

Walk as if you are heading back towards the Temple of the Ocean King. Just southeast of the Temple’s entrance, there is a cave that we recently blew open. If you haven’t done so already, blast away at it using a bomb and then enter the cave.

Jump across the platforms and next to the treasure chest, you will find an eye switch. Hit it with an arrow and it will cause a bridge to extend across the water. Cross the bridge and defeat the Zora Warrior that is found here. Exit the cave to the south.

There is a tablet just to the left that has a secret, telling you to draw a line from the Mercay Tavern to the Temple of the Ocean King. There is a nearby weak spot that if you draw a parallel line, it will lead to a secret.

Glance to the left and you’ll see an eye switch, but it is higher up. Climb the steps to the right and then hit the eye target with an arrow. This will cause a nearby statue to appear. Before hitting the statue, run around the corner, going south a screen and you’ll find a pair of treasure chests that contain a ship part and a big green rupee.

Return to the statue and hit it with your sword to activate it. Turn the statue so that it is facing in the north-northwest direction. Follow the light and it will be shining directly on the wall. Toss a bomb at this wall and it blow open a secret cave. Inside of the cave, you can just run across to the east and exit.

Optional: Courage Gem #6

Inside of the cave, run over to the bridge and then pull out your Boomerang. Aim southward and you’ll see there is a crystal switch across the water. Hit the switch and it will cause a treasure chest to appear. Run on over and open the chest to get a Courage Gem.

Optional: Freedle Tag Mode

Back outside, you can climb the steps to meet with Freedle, which opens up the Tag Mode feature of the game. This is a multiplayer feature which allows you to trade treasure and ship parts with friends. It isn’t required at all and is just a bonus. Walk to the southern end of this island and step on the floor switch, causing a bridge to extend to the main portion of Mercay Island. This will allow quick access to Freedle at any point.

Optional: Wisdom Gem #7

Just to the east of Freedle, at the northeast corner of Mercay Island. Walk to the right side and open the treasure chest here to get a Wisdom Gem.

Optional: Wisdom Gem #8

Return to Linebeck to set sail. Our next destination is over at Bannan Island where we want to deliver Jolene’s Letter. Make your way to the island and then enter the Old Wayfarer’s hut. Show Jolene’s letter to Joanne and she will thank you by giving you a Wisdom Gem.

Our next destination is the dreaded Ghost Ship. Begin by venturing into the Northwest Quadrant and then sail towards the fog at the western portion of the area. When Link gets deeper into the fog, suddenly Linebeck’s ship will stop working. After a short talk with Linebeck, the three spirit fairies offer to help find the Ghost Ship. The ship will automatically move forward and Link can steer it left or right. The three spirit fairies will begin to flutter and go wild when you are headed in the direction of the Ghost Ship. Keep turning until the fairies are going wild and then head straight forward. This can be a tad tricky as remember, the Ghost Ship itself will move, so you are you sailing towards a moving object. Eventually you will find the Ghost Ship and you will climb aboard.

There are a few Keese on the deck of the Ship, but they can be ignored. Just step down the entrance to the left.

Once you enter, walk to the left and door will immediately close behind you. Three Poes will appear and will shoot blue fireballs out at you. Just quickly attack them before they disappear. After all three have been defeated, walk to the left and speak with the first daughter of the great house of Cubus. She asks you to save the three remaining sisters from the Cubus family.

Take the pathway to the north and watch out for the Skulltula. These spiders will drop from the ceiling and they can easily be defeated with a sword swipe, or a hit with the Boomerang. Pull out the Boomerang and use it to hit the crystal switch just above, causing the nearby spikes to lower. Make your way eastward, avoiding the blue fireball that appears. There is a second crystal switch above that you can hit with your Boomerang, and this will cause the nearby spikes to lower.

At the end of the pathway there are flames that block your way. Fortunately you are able to leap across the gap just to the south to reach the southeast portion of the room. Make your way around the corner of this room, avoiding the floor spikes that rise. Hit the nearby crystal switch, causing the spikes to lower. Before heading up, open the treasure chest to get a triangle crystal. Carry the triangle crystal and jump back across the gap. Place it into the triangle pedestal located just above where the flames are. This will cause the flames to lower.

Return to the treasure chest and head up to find the next member of the Cubus family. She will now follow you and will ask you to take her back to her sister. While following you, she will get creeped out every time a Skulltula draws near. At this point you’ll have to defeat the enemy and then talk to the sister again. Take her through the winding pathway, heading back to the western portion of this room.

After uniting the sisters, they will ask you to bring back the two remaining sisters. Return to the east end of the room and head down the staircase to get to the lower floor.

The second floor of the Ghost Ship is filled with safe zones, much like the Temple of the Ocean King. Travel eastward and a massive Reapling will appear. These enemies move around much like Phantoms and their line of vision can be seen on the map above. They cannot be defeated and instead, if Link strikes them, they will be stunned for a short period of time. If a Reapling spots Link, it will quickly move towards him, swinging its massive scythe which will deal two full hearts of damage. Fortunately, these enemies cannot enter the various safe zones in the area. Travel eastward and make your way through the room, avoiding the Reaplings, spiked floors, and the Skulltulas along the way. At the northwest end of the room, you’ll find the next Cubus sister.

After meeting with the Cubus sister, strike the nearby orb, causing some nearby spikes to lower. The sister tells you to pick the left chest, but naturally, something seems rather suspicious about the way she talks. Pick the right treasure chest to get a Yellow Potion. If you pick the left one, you’ll get a black Rupoor, which takes away 10 rupees. Furthermore, it will cause a second Reapling to appear in the room.

Backtrack to the staircase at the south end of the room. This time however, we can pass through the central part of the room as the spikes are lowered. Open the nearby treasure chest to get the round crystal. Carry the crystal back up to Floor B1.

Back on Floor B1, place the round crystal into the nearby pedestal, causing the flames to lower. This creates a shortcut to guide the Cubus sister back to the other two. Along the way, there is a treasure chest at the south end of the map. You could have gotten this earlier but if you haven’t, jump on over and open the treasure chest to get some random treasure. Reunite the Cubus sister and the three will then tell you to find the final sister. Return to the stairs at the east end of the room and head back down to Floor B2.

This time around we want to make our way to the southwest part of the room where you will find a staircase. It’s a rather straight shot, as long as you didn’t cause a second Reapling to appear. Make your way over and head down the steps to reach Floor B3.

There are a few levers here that we will get to in just a bit. Walk eastward and the door will close behind you. Quickly make due of the five Skulltula enemies and the nearby flames will lower. Nearby there is a crystal switch, but you don’t actually need to hit it. Doing so will cause some spikes to lower, but it will also cause a Reapling to appear. Just ignore it. Instead swing around the corner to another safe zone just above the spikes and read the stone tablet. It gives the proper order to pull the levers in: 2 4 5 1 3.

Return to the south end of the room and pull them in the proper order. From left to right pull them…

1. Pull the fourth lever
2. Pull the first lever
3. Pull the fifth lever
4. Pull the second lever
5. Pull the third lever

Doing so will cause the upper spikes to lower, allowing you to reach the center part of the room. Lift some of the barrels that are in the way and step on the floor switch that is somewhat hidden to the west. This will cause the purple flames in the room to disappear. Make your way over to the northwest corner of the room. Along the way you will find a safe zone with a treasure chest, containing a Purple Potion.

At the northwest corner of the room there are a number of barrels, one of which is fluttering. Lift up the barrel to find the final Cubus sister. Guide the sister back up to Floor B2, and then all the way back to Floor B1. Take her to the west end of the floor and reunite her with her sisters.

After a short talk, you’ll appear back outside where the sisters want to play a game of dead man’s volley. This will trigger the boss battle with the sisters.

The battle is similar to many previous boss battles in the Zelda series. The sisters will shoot balls towards Link and he’ll have to deflect them back with his sword. As the battle goes on, the sisters will shoot balls out much quicker. During the first phase, three of sisters will shoot out lasers, while the red sister will toss balls towards Link. Just hit two balls back at the red sister and she’ll be defeated.

During the second phase, two of the sisters will shoot beams towards Link, while the third one will toss an energy ball. They’ll occasionally toss a new type of energy ball, this one looking like it was made of a bunch of smaller balls. Just avoid this one as you cannot reflect it back. Reflect the standard ball back and they’ll volley it among each other, before sending it back towards Link. Each time they send it back, reflect it back with your sword until it hits one of the sisters. Repeat this phase until you’ve hit at least one of the sisters two times to defeat her. When there are only two sisters, the battle is pretty much the same. Since there are only two though, the reflections happen a bit more rapidly.

In the final phase, the last remaining sister will toss three energy balls towards you, in which you can only deflect one of them back. Just do so and continue the volley until you’ve hit the sister. Repeat this same process until the final sister has been defeated.

After they’ve been defeated, walk over and grab the Ghost Key. Open the treasure chest to get a Heart Container and then step into the blue portal. Back inside, head down to Floor B2 once again. At the northeast corner of the room, use the Ghost Key on the lock and then head up the staircase. Enjoy the lengthy cut-scene and skip ahead to the next chapter where we will once again re-visit the Temple of the Ocean King.