Someone with the power to stop Skull Kid is in the Woodfall Temple, which you can reach from the Southern Swamp. You can get into the temple after going to the Southern Swamp and helping Koume, taking a boat cruise to the Deku Palace, and meeting the captured monkey.
Make sure that you have gone to Woodfall and hit the owl statue there with your sword so you can warp back there any time.
To have as much time as possible to finish the dungeon, use the Song of Time to go back to the Dawn of the First Day, then use the Song of Inverted Time (play the Song of Time backward) to slow the flow of time, then use the Song of Soaring to warp to Woodfall Temple. This should give you about three hours of real world time to finish the dungeon.
Enter the Temple
From the owl statue in Woodfall, be sure to transform into a Deku Scrub and play the Song of Awakening while standing on the Deku symbol if the temple is not open. Then, as a Deku Scrub, go into the nearby flower and float to the temple entrance. Go inside.
Catch a Stray Fairy
There is a fairy right in front of you in the entrance of the temple. Wear the Great Fairy's Mask to make the fairy come to you. If you don't have the Great Fairy's Mask, you can go back to Clock Town and find the Stray Fairy that is floating in the Laundry Pool if it's daytime or in East Clock Town if it's night. As a human, take it to the Great Fairy's Fountain. She will give you the Great Fairy Mask.
Back inside the first room of the dungeon, you can break the pot here to find a normal fairy. If you use your bottle to catch the fairy, then if you die, the fairy will bring you back to life. The fairy will disappear after reviving you.
Catch a Second Stray Fairy
You need to float across using the Deku Flower, but if you fall to the bottom, just go toward where you entered the room, and use the ladder to go up. There are Black Boes on the floor, but they are easy to defeat.
Transform into a Deku Scrub and use the nearby flower to float to the right, where there is a platform with a small treasure chest on it. Open the treasure chest to find another Stray Fairy.
Catch a Third Stray Fairy
Use the nearby flower to float to the next flower platform. Continue floating until you have reached the far side of the room, but be careful: there are two Skulltulas to either side of the exit. When you have safely reached the exit, go through.
In the next room, the water is poisoned, so if you fall into it while in human form, your life will slowly be drained and it will be difficult to get out of the water. To be completely safe, stay in Deku form in areas with poisoned water.
To the left of the door that you entered through, there is a Deku Baba. You can kill it to get a Deku Stick. This Deku Baba will grow back after you kill it, so you can get unlimited Deku Sticks here.
Go down the ramp past the Deku Baba. There is another Deku Baba at the bottom. When you kill it, a Stray Fairy appears.
Get a Fourth Stray Fairy
Transform into a Deku Scrub and hop over the water to go to the small flower that is floating there. If you jump onto one of those flowers in human form, it will close up and bite you. As a Deku Scrub, continue hopping from flower to flower. At the end, there is a ledge with a door on it. Before going through the door, become a Deku Scrub if you aren't already, and hop from the ledge to the platform in the corner that has five pots on it. Break the pot closest to the corner to find a Stray Fairy.
Get a Key
Hop back over the water to the nearby ledge, then go through the door.
As a Deku Scrub, hop to the flower in the middle of the room. Use the flower to float to the treasure chest to the left. Open the chest to get a key.
Get a Fifth Stray Fairy
While still on the ledge where you got the key, look at the wall to the left of the chest and you will see a beehive. As a Deku Scrub, spit a bubble at that beehive to make it fall into the water. It will break open and a Stray Fairy will come out. Wear your Great Fairy Mask to make the Stray Fairy come to you.
Get the Map
From where you got the key, hop down to the water and hop onto one of the large flowers. From there, hop to the flower in the middle of the room and float to the north part of the room where there is a door. Go through.
The door will lock behind you. You have to kill the Snappers here. One way to kill them is to dive into a flower as a Deku Scrub and wait for the Snapper to be on top of the flower, then jump out of the flower. Alternatively, you can throw a bomb at a Snapper or use the Blast Mask to make the Snapper flip over, then hit it with your sword until it dies. After all of the Snappers are gone, a treasure chest will appear. It contains the Map.
Get a Sixth Stray Fairy
Exit the room that you got the Map in. As a Deku Scrub, hop back to the south exit of the room and go through the door.
As a Deku Scrub, hop across the flowers in the water to reach the ledge with the locked door. Go through the locked door.
As a Deku Scrub, look up at the ceiling above the stone block up ahead. There is a beehive on the ceiling there. Spit a bubble at it to make it fall. A Stray Fairy comes out.
Get a Seventh Stray Fairy
Stand next to the stone block and put a bomb there, or use the Blast Mask there. There is a Stray Fairy trapped in a bubble under the bridge here, and using a bomb at this spot will pop the bubble. Use the Great Fairy Mask to make the Stray Fairy come to you.
Get an Eighth Stray Fairy
Walk up to the large stone that has the mask symbol on it. Push it forward to get it out of the way. Go to the right and follow the narrow wooden bridges to reach a Skulltula and a torch. Kill the Skulltula to get another Stray Fairy.
Open the Door
From the torch, go along the wooden bridge that you haven't walked on yet, and follow the path to reach the stone that you pushed earlier. Push it forward until you can't push it anymore. Then go back to the torch. You can kill the moths using a bomb or the Blast Mask. Equip a Deku Stick. You need to be in human form to equip it. Walk past the torch to make the stick catch fire. If you didn't kill the moths, don't stand still, because the moths will follow you and hurt you. Run with the burning stick to locked door. Light the torch in front of the door. The door will open. Go through.
Get the Compass
In this room, there are two Dragonflies. Kill them by spitting bubbles at them or hitting them with your sword when they come down, then open the treasure chest that appears. You will get the Compass.
Get an Ninth Stray Fairy
Leave the room where you got the Compass. Use a Deku Stick on the torch to light it, then go left from the door of the Compass room, across the wooden bridge, and up some stairs to where there is another torch. Use your burning Deku Stick to light it, then put the Deku Stick away by swinging your sword.
Take out another Deku Stick and light it with the torch up above. Jump across the platforms to go to the spiderweb. Light it on fire with the Deku Stick, then put the stick away.
Kill the Deku Babas just past the spiderweb to get some Deku Sticks. These Deku Babas regrow, so you can get unlimited sticks here.
The next room will be dark, so you might want to light a Deku Stick with the torch near those Deku Babas before going up the stairs. When you are ready, go up the stairs. There are a bunch of Black Boes in this area. You can use Deku Sticks to see more clearly. If you kill all of the Black Boes in the room, a chest appears that contains a Stray Fairy.
Light the Torches
There are three torches in this dark room. Each torch is next to the wall. Light a Deku Stick and go around the wall to light the three torches. Then go through the door that opens.
Get a Tenth Stray Fairy
There are a couple of Dragonflies in this large room. You can try spitting bubbles at them to get rid of them. As a Deku Baba, use the flower near the entrance to float to the moving flower platforms in this room. Make your way to the corner of the room where there are some stairs. Go down.
Go to the right and you will see a Stray Fairy trapped in a bubble. Pop the bubble to get the fairy out.
Get a Eleventh Stray Fairy
Go to the switch on the floor that was straight ahead when you first entered this room. Step on it. Ladders will appear, giving you a shortcut to the lower floor.
Go to the flower on the upper ledge near where you rescued the stray fairy in the bubble. As a Deku Scrub, float over to the switch that is on a tree branch nearby that has a torch on it. Transform back into a human to become heavy enough to activate the switch. A chest will appear on the other side of the room. Go over to that treasure chest and open it. There is a Stray Fairy inside.
Get the Dungeon Treasure
Go back to where you stepped on the switch to make ladders appear. Go through the door next to that switch.
Go to the right, to where there is a flower in front of the door. Don't use the flower yet. For now, go into the door.
The door locks behind you, and a Dinofols attacks. It can do jump attacks with its sword, and might jump behind you before attacking. After you hit it, it will spit fire unless you hit it again before that. You can stun it with Deku Nuts, or with Deku Link's spin attack. You can hurt it with the sword, or with Deku Link's bubble attack. It is also vulnerable to bomb blasts.
After the Dinofols is gone, open the chest that appeared. You will get the Hero's Bow. Exit the room.
If you didn't get the Stray Fairy in the westernmost room on 1F where you pushed the stone on the wooden bridge, go back there and use the Hero's Bow while standing near the door that had bars on it. From there, shoot the bubble under the bridges to free the Stray Fairy. Then wear the Great Fairy Mask to make the fairy come to you.
Reach the Mini-Boss
Go back to the room just before the Dinofols room where you got the Hero's Bow. As a Deku Scrub, jump down to the flower in the middle of the water down below. Then take off the Deku Mask and equip the Hero's Bow. Shoot the diamond-shaped target on the ledge across from you. The platform in the middle of the room will rise up to your level. As a Deku Scrub, use the flower on the moving platform to float onto the far ledge. Go through the door there.
Gekko and Snapper
The door locks behind you. A Gekko attacks. You can stun it with Deku Nuts or the Deku Scrub's spin attack. Hit Gekko a few times with your sword. Then the Gekko summons a Snapper and rides on top of it. You need to flip the Snapper over. One way to do this is to transform into a Deku Scrub and dive into a flower, then pop out when the Snapper goes over the flower. Another way to flip it over is to use bombs or the Blast Mask.
When you successfully flip the Snapper, the Gekko will fall off and start climbing on the wall. Transform back into a human. Use Z-Targeting to target the Gekko, and use the bow to hit the Gekko when it stops moving. Repeat the process until the Gekko and Snapper are defeated.
Get the Boss Key
Go into the door that opened. Open the big blue chest to get the Boss Key.
Get a Twelfth Stray Fairy
Leave the Gekko room, then turn into a Deku Scrub and float to the door to the right. Go through the door on the west side of the upper floor.
In this room, transform into a human and use your bow to shoot an arrow at the torch on the wooden flower down below. You need to shoot the arrow such that it goes through the burning torch before it hits the unlit torch in the middle of the wooden flower. That way, your arrow will catch fire and will light the second torch. When you light the torch on the wooden flower, it will rise up and start spinning. Go onto the flower, either by jumping across the ledge or by using a flower as a Deku Scrub. Then as a human, use your bow to shoot an arrow through the torch in the middle of the wooden flower, hitting the unlit torch on a branch on the side of the room. This will unlock the north door of the room. Go through.
Use your bow to kill the Dragonflies in this room. Also use your bow to pop the bubble that a stray fairy is stuck in, near the middle of the room.
Get a Thirteenth, Fourteenth, and Fifteenth Stray Fairy
Climb down the ladder. As a Deku Scrub, use the flower to float to the ledges next to the ladder. Three of the alcoves have a Stray Fairy stuck in a bubble. Pop the bubbles to catch the fairies.
Reach the Boss Door
Use the flowers to enter the upper southeast alcove. From there, use the bow to shoot the crystal switch, then become a Deku Scrub and float to the flower that you revealed when the flames were lowered. Be careful, because the flames will reappear after a while. Use the flower that the flames were blocking to float to the flower on the roof above the crystal switch. From there, float to the boss door. Go in.
Go toward the center of the room and Odolwa will fall from above. Don't get too close to Odolwa or he might bump you with his sword, kick you, or swing his sword at you. If Odolwa is dancing, summoning monsters, or moving around, he is vulnerable. You can shoot Odolwa with an arrow to stun him, then run over and hit him with your sword (or just hit him with your sword without stunning him if you prefer). You can block some of Odolwa's attacks with your shield. You can also harm Odolwa with Bomb Flowers, which can be found around the room. The Bomb Flowers eventually grow back after you take them. Another way to inflict damage is to transform into a Deku Scrub and hide in the flower in the middle of the room, then pop out when Odolwa is above you. As a Deku Scrub, you can stun him by spitting bubbles at him or using the spin attack. If Odolwa summons moths or spiders, throw a bomb to make the creatures go toward it. They will die when the bomb explodes. Odolwa can also make rocks fall from above. In addition, Odolwa can make a temporary ring of flames appear around you.
After you defeat Odolwa, get the Heart Container. Then enter the glowing light and you will receive Odolwa's Remains.
Learn the Oath to Order
Watch the cut scene.You will learn the Oath to Order during the cut scene.
Rescue the Deku Princess
Cut through the vines to find the Deku Princess. She asks you to carry her in something so you can take her back to the Deku Temple. Catch her inside of a bottle, then go outside.
Walk straight down the ramp and through the exit at the end. The Deku Temple is straight ahead, so climb down the vines in front of you to reach a lilypad, and go from there to the Deku Temple.
As a Deku Scrub, enter the temple, and go to the King's chamber. Let the princess out of the bottle.
Get the Mask of Scents
After a cut scene, you will find out that the Deku butler put a reward for you in the shrine that is to the right when you exit the palace. So leave the palace and go to the right to find the entrance to the shrine. Go in.
Go up ahead and talk to the butler. He will lead you to the reward. However, he moves very quickly. It helps to have the Bunny Hood. The reward is the Mask of Scents. Wearing it makes your sense of smell stronger. You can use it in the Woods of Mystery (where you found Koume) to find fragrant mushrooms that you can catch in your bottle. While wearing the mask, if there are any mushrooms in the area, you will see purple smoke on the ground. Use a bottle there to get a mushroom. Then you can talk to Kotake in the potion shop and give it to her. Then leave her shop and go back in. She will be selling blue potions, although she will give you one for free the first time you get one from her.
Go to the Next Dungeon
Make sure you have some bombs and arrows. Go to North Clock Town and talk to the soldier to use the north exit. Go straight ahead to an area of snow and ice. Go down the ramp to the left. There are Dodongos down below. Go north and walk up the ramp to the upper level. There is some ice blocking the path. Shoot the icicle twice with your bow. The ice blocking the path will shatter. Go past where the ice was.
Follow the path in this next area, avoiding Tektites. At the end, snowballs block the way. Use a bomb to get rid of the snowballs. Continue along the path and turn left after the wooden sign. Keep going to reach Mountain Village.