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The Cheval Rope and Flippers
The Maku Tree will tell you that she senses an Essence on Crescent Island to the south. However, you can't swim, so you'll need to find some sort of vessel to take you there. Go east, north, west, then north. Jump over the pit and go north twice, then into the cave. There's obviously a Piece of Heart here that you want. Jump counterclockwise around the room. When you reach the platform to the right of the Piece of Heart, lift the pot, then go to where it was and jump to the left. Grab Piece of Heart #5/12. Jump south twice, then lift the pot and jump to the exit and leave.
Now go back to Lynna Village. Go out the northeast exit. Go south four times, then jump over the river and go north. Go into the house and talk to the guy in here. He will say that his name is Cheval (how would one pronounce that?) and that his dream is to create flippers and rope that won't decay in water. Now leave the house to find Ralph, who will say that he's seen a grave that has Cheval's name on it in the present. Then he'll run off and do some stuff that clearly won't be of help seeing as you're the one gathering the Essences.
Now go south, west, west, north, southwest, south, south, and into the building. Talk to the guy in here and he'll explain that his name is Rafton, and his dream is to make great rafts (his parents sure knew what they wanted him to do when they named him). However, to do so, he needs some rope that won't decay in water, which incidentally Cheval just happens to be working on. Clearly you're gonna need that rope.
However, Cheval isn't done with it, so you're going to have to go into the present, which I reckon is about 380 years after Cheval's death. Ralph said that he saw a grave with Cheval's name on it, so head to Yoll Graveyard. Go north to find an area with a whole bunch of pits. You can't get across these with just the Roc's Feather. Go south, then east. A bunch of Ghinis are terrorizing a blue bear with wings. Kill the Ghinis, then talk to the bear. He says that his name is Moosh. You can ride on him. You can make him fly by repeatedly pressing A, and by holding A then releasing, he will do a ground pound.
Go back to the area with the pits and use Moosh to fly over them. When you reach a grave in the northwest corner near a rock, push it north. There's a secret staircase under here. Gee, that's original. Go down, and it's revealed that this is a big watery cave. Kill some enemies, then go north, east, and south. Jump to the east, then to a big yellow thing sticking out of the wall. Grab it with the Power Bracelet, then pull it back until you can't pull it back anymore. Jump to the east, then run between the blocks and to the Zora's Flippers. You can now swim! When you're in the water, you can dive with B and swim faster with A.
Now swim north and around some gnarled root looking things. Go west and onto a platform. Grab the Cheval's Rope that's here. Now leave the grave, lift the rock, and go south. Moosh will say goodbye. Now go back to the past and bring the rope to Rafton. However, he says that you need something else...a chart.
Leave the building and go north. You'll run into Ralph again. He'll tell you that a weird guy has sea charts to the secret island. Hm, that sounds suspiciously like what we need. Isn't it convenient how Ralph just happens to know all this stuff and encounter us just as we need the information? He'll run off saying that he needs to help Nayru. Sigh...he's so useless, yet so helpful at the same time :)
Anyway, go back to the present. From there, leave through the southern exit, to the Ember Seed tree. Go south, lift a rock, and go south again. Now go east, then north. Jump over a pit and go north again. Here, you can see a man in a green outfit being held up by a balloon. If you're a Tingle-hater, I feel very, very sorry for you, because yes, he is indeed the "weird man" with the chart you need. Go east, then north. There is a kangaroo here. Talk to him and he will say that his name is Ricky and he lost his gloves. He thinks that he left them by the tree at the beach, but of course he can't find them because you need to find them for him. Go south, west, south, south, and west. Use the shovel to clear the patches of dirt away. The gloves should fall out of one of them. Pick them up, then bring them back to Ricky.
You can now ride him the way you rode Moosh. However, he is entirely different from Moosh in terms of his abilities. He can jump over small holes and scale cliffs as long as there's no rail on them. He also a pretty good fighter. Go south, then west, and scale the cliff here. Go south, jump over the hole, then go north. Scale the cliff and jump out of Ricky's pouch. Jump and slash in midair to pop Tingle's balloon. It will explode rather exaggeratedly and Tingle will fall down and look around. Talk to him and he will talk about how he is a reincarnation of a fairy even though he's 35. Then he'll ask you if you want him as a friend. This is why I feel sorry for you if you're a Tingle-hater, because in this game you actually have to agree to be friends with him. It may be difficult, but force yourself to say yes. He will give you the Island Chart. He will also tell you to come back when you have more Mystical Seeds.
Ricky will remark that because you got what you wanted, he's out of here because he can't stand Tingle. Go back to the past and present Rafton with the chart. Now leave through the southeast exit and get on the raft. Go south and you'll see a bunch of whirlpools. You can't get past those. Ever. In any part of the game. Go south again, then east, north, and north. A cutscene will occur of a huge storm. Humorously, several monkeys fly by. Not so humorously, Link gets struck by lightning. Ouch.
Link will wake up to find several lizard-like creatures around him. These are the Tokay, the residents of Crescent Island. He jumps up and they back away...before pulling out Link's stuff! They just stole all your items and are running off with them. You have to find them one by one and get all your items back. This section is pure genius, by the way.
Well, first go south and push the bulb-like thing here twice to the right. Then go east. There's a Tokay on a cliff with your Seed Satchel! Sadly, you can't reach it from here. Instead, go south. Talk to the Tokay here to get your shovel back. Now go north and into a cave. There's the Tokay with your sword! You could easily cut your way through the crystal things here, but sadly the very item you need to do that is just out of your grasp.
Instead, go to the north wall, the push the block west. Dig through the mound of dirt, then go south and talk to the Tokay to get your sword. Now cut your way back to the entrance. Go west, north, up the stairs, then east, south, and east. Talk to the Deku here (it's hiding under a patch of grass) to buy a shield for 50 rupees. That's steep, but the next opportunity you get to buy it at a store won't be until after you complete the next dungeon. You won't get your old shield back for a long time, so you're going to have to make do with this one.
Go south and push the bulb north twice and west four times. Then go south, down the stairs, east, and north. Hey, here's a time portal, maybe we can go into the future and - oh wait, we don't have the Harp of Ages. What a tease. Go north twice and into the building. This Tokay has your Roc's Feather and Power Bracelet. You can get the feather back for 10 Mystery Seeds. Ok, we'll pay up - oh yeah, we don't have the Seed Satchel. ARRGGGHFGWEIOGO!!!!!!!!!! However, it offers to trade it for you shovel instead. Say no, and instead examine the Power Bracelet. The Tokay offers to trade it for 10 Scent Seeds. You wouldn't even have those if you had your Seed Satchel. However, trade your shovel for the Power Bracelet.
Leave the building, then go south, south, south, west, up the stairs, east, north, and lift the rock, going into the cave. Push the bottommost block east, then the one directly above it also to the east. Go up the stairs. Here are your bombs! Now go back downstairs and bomb the cracked blocks and open the chest for a Gasha Seed. Go up the left flight of stairs, then go back to the building to trade your Power Bracelet for the Roc's Feather. Now go south, south, south, west, and jump across the pits here to the west. Go north, bomb the wall, and go in the cave.
You can immediately see a Tokay with your Flippers. Throw a bomb north to blow up some cracked blocks. Then jump across. Go around some rocks, then jump to the right and throw a bomb south to a cracked block. Jump south, the east. Talk to the Tokay to get your Flippers back. Go all the way back to the trader and trade your Roc's Feather for the Power Bracelet. Before doing anything else, however, go south and bomb the wall here. Go in the cave and talk to the Tokay to start a minigame. All you have to do is throw meat at Tokay passing on your left and right. Not that difficult all in all, but watch out and don't get lazy. After winning, you will be awarded the Scent Seedling. Could this be related to the Scent Seeds you need to trade for your Power Bracelet? Nah, can't be.
Now leave, then go south, south, west, north, north, west, north, and east. Lift the rocks, then talk to the Tokay here. It will help you plant your seedling, then tell you to come back after a long, long time. Great, we just need to go forward in time - oh wait, but you don't have your Harp of Ages. Darn. Anyway, go east, south, west, south, west, and into the cave. Swim to the northwestern rocks, lift them, then go to the deep patch of water. Dive down, then swim to a ladder. Climb up a few until you come out of the 2D screen. Lift a rock and go to another staircase. Go west to finally get that Seed Satchel that the Tokay has been taunting you with since the beginning. Go back to the trader and give it 10 Mystery Seeds to get your Roc's Feather back for good. You now have both the Roc's Feather and the Power Bracelet! The Tokay's still got your shovel though. You'll have to do something about that later.
Now leave, then go south, south, south, west, west, and into a cave. Lift some pots and go down a staircase. Swim to the left until you reach a ladder, then climb up. Fall to the right onto a moving platform. Then jump across some platforms with the Roc's Feather, then up a ladder. Leave the cave. Hey, the Tokay with your Harp of Ages is here! Talk to it to get back the power of time. Wow, that sounded really cheesy, but whatever. Go to the area two squares south of the trader, then play the Harp of Ages on the Time Portal.
Now you're in the present and the island has a much more tropical feel. Go south and talk to the Tokay here. He will say that he has to cook, but his nose is all stuffed up, so he can't smell what he's cooking. If you give him the Stink Bag, he'll be "stimulated" by the smell. Unsurprisingly, it clears up his nose. He gives you the first item in this trading sequence that is better than the previous item: the Tasty Meat. Mmmm, that looks really good. Sadly, you'll never get to eat it.
Leave the building, then go west, north, north, west, and down a vine. A Tokay will bother you for no reason, saying that it takes a long time for trees and vines to grow. Wow, really? Go west, up a vine, east, and east. Here's the fully grown Scent Seed tree! Slash it to get some Scent Seeds. These are almost entirely useless, except for getting your shovel back, but they apparently attract monsters. You can immediately see why these things aren't very useful. Jump down the cliff, then go east and south twice. Play the Harp of Ages and go into the Time Portal.
Go back to the trader, then trade your shovel for the Power Bracelet and the Power Bracelet for 10 Scent Seeds. Congratulations, you now have all your items back! Now leave and go south, south, south, west, west, and into the cave. Go through here again, then when you emerge, go north, west, and south. Dig through the mounds of dirt and play the Harp of Ages on the time portal. Go north, north, north, east, south, south, northeast, and into the building here.
This is my favorite dungeon in the game :D
The Four Crystals
First go to the northwest corner. Push the middle west block west, then bomb the cracked northwest block. Go west. In this room, you will encounter a new type of enemy called Pols Voices. They resemble large bunny heads. They are immune to your sword, but they have sensitive ears. Play the Harp of Ages and they will instantly die, causing a chest to appear. Open it for the Dungeon Map. Go back east, then bomb the northwest block, and push the northeast block east. Go north.
Kill the Mini-Moldorms here and go east. In this room, there are a few red creatures wearing masks (you have to slash them from behind; you'll get an item that can remove their masks later), as well as a funky looking blue crystal. Slash the crystal and it will say that it sounds like something far off was knocked loose. Go north. This is an interesting theme in this dungeon. In this room is a dial. When you step into it, it will spin once, either clockwise or counterclockwise. When the dial is blue, it will take you counterclockwise. However, as soon as you step into it, the dial will turn red. If you step back into it, it'll take you clockwise, in other words where you just came from. However, if you somehow find a way to loop around back to the original place where you came from, the dial will still be red - meaning that if you step into it, it'll take you clockwise instead, i.e. a new area.
Step into this dial and go east. Go to the far east wall, then bomb the cracked block here. Throw a bomb across to another cracked block that the previous cracked block was blocking (no pun intended). Go to the northern wall and push the block here south. Throw another bomb south to a cracked block. Now go to the south wall and push the block directly below the cracked block you just blew up, and push it north. Slash the crystal. Now push the block to the right of it north. Push the statue here east, east, north, north, west, and south. Grab the key that appears.
Now go west and back into the dial. Go south, west, and north. Fall into the pit here, then kill the enemies. Go south. There is a Mini-Moldorm in a small walled-off area. Slash it from across the barrier until it dies. Then go south. There are some Pols Voices here. Play the Harp of Ages to get rid of them, then go northwest. Throw a couple of bombs at the Mini-Moldorm, then go southwest, then west. Here, there's a switch that you can't reach. It is by a moving floor. You have to throw a bomb, but time it so that the bomb will blow up near it and not ride the moving floor past it. After you hit the switch, a statue will start moving. Kill it with a bomb, then open the chest that appears to get the Compass. Then go up the stairs.
Go west. Push the north block north, the northwest block west, and the northeast block east. Grab the key that falls. Now go east, down the stairs, east, north, and up the stairs. Slash the crystal here, then push the block that's jutting out to the east. Go east, then go into the dial. Go south, west, north, east, and back into the dial. You'll end up on the north end, which you oridinarily wouldn't be able to get to. Go north. There is a new type of enemy. They are called Like Likes and they are very dangerous. They can't do any damage to you, but if you touch them, they will eat your shield. Unlike in the 3D games, there is no way to get it back after they eat it, no matter how fast you kill them. Cautiously kill them, then go east.
Step on the switch in the northeast corner, and all the statues will come to life. Kill them all with bombs (it may take a while, as they have an irritating habit of walking away from your bombs), then grab the key. Go west, then north. In this room, you will encounter Flying Tiles. They are fake tiles that will fly at you one by one. To avoid being hit, stand in the southwest corner, face to the right, then slash your sword repeatedly. Go west, south, northwest, up the stairs, south, and open the chest for 30 rupees. Go back north, then open the locked door. Go west. There are some Mini-Moldorms, as well as some new enemies called Arm Mimics. These enemies will mirror all your movements, only in the opposite direction that you are going. Just slash them until they die. After you kill all the enemies, open the chest for the Seed Shooter.
With this item, you can shoot Mystical Seeds in any of the eight main directions (north, northeast, east, southeast, south, southwest, west, and northwest). Once they hit a wall, they will ricochet. After hitting three walls, they will stop. There are certain seeds you must shoot to complete certain tasks, but for general use (such as hitting faraway switches), Scent Seeds are best because they are used the least for their intended purpose. If you run out of Scent Seeds, go to Mystery Seeds. Anyway, go east. Try out your new item by firing an Ember Seed at to light the torch in the middle of the room. Then go south and east, then take care of the Flying Tiles yet again. Go south. Now you can hit this crystal. You have to fire a seed diagonally so that it ricochets into the crystal, and it will say that something heavy fell.
Go south to find that the dial is gone. In its place is a chest, which you can open for a Gasha Seed. Then go west, fall down the pit, and go east. The dial is here. It must be the heavy thing that fell! Step into the dial, then go south. There are a bunch of blocks here, and some torches behind them. Go to the east side of the block-barrier, and push the three eastern blocks west and into the pit. Shoot some Ember Seeds and try to ricochet them at the torches. Open the chest that appears for a Gasha Seed. Now go west, north, and east. Step into the dial and go north twice.
This miniboss fight is simple. Just equip your shovel and sword. When the miniboss goes underground, use your shovel on it. Then slash it with your sword. Repeat until it dies.
Getting to the boss
Go west, then north. Kill the Mini-Moldorms, then push the northeast block west. Grab the key that falls, then go south and east. Step into the portal. Then go north, north, fall into the pit, go east, into the dial, south, and west. Kill the Mini-Moldorm, go south, kill the Pols Voices, then go northwest, north, up the stairs, south, south, and into the portal. Go south twice, then into the dial. Go east. Step on the switch, step off the switch, and step on it again. Shoot a seed northeast. Go north and open the chest for the Boss Key. Jump down and go west, then south. Go into the dial, then go west and north.
Slash the switch once, then shoot the diagonal red thing. Your seed will ricochet to a lever that will create a bridge. Cross the bridge, then slash the switch here twice. Shoot the diagonal red thing. Go south across a bridge and open a chest for 20 rupeees. Go north through a locked door. Shoot a western switch, then shoot the diagonal red thing. Go across the bridge, slash the switch twice, then shoot the diagonal red thing again. Go north, then west.
Boss: Shadow Hag
The boss will begin by splitting itself into four shadows. If you touch any of them, you will take damage. Eventually, they will merge and the shadow will disappear. Butteflies will appear occasionally appear throughout this boss fight. At some point, the Shadow Hag will appear behind you. You will probably feel tempted to turn around and slash it. Don't, because as soon as you look at it, it will disappear. Instead, shoot a seed directly in front of you. It will bounce off the wall and hit the Shadow Hag. Just repeat until it dies. After it dies, grab Heart Container #3/8. Go west, then grab the Echoing Howl.