You can reach the Stone Tower from Ikana Canyon. You have to complete the Ikana Castle mini-dungeon to learn the Elegy of Emptiness, then complete the switch puzzles to reach the owl statue. Read the Ikana Castle section to find out how to reach the owl statue.
Prepare for the Dungeon
I strongly recommend buying some Chateau Romani milk and drinking it before entering this dungeon. When you drink it, you get infinite magic power until the next time you play the Song of Time to return to the Dawn of the First Day. This is helpful in any dungeon, but especially this one. You can buy Chateau Romani if you have Romani's Mask. If you don't have it, read the instructions on how to get Romani's Mask. Then go to the night of the First Day and wear Romani's Mask to get into the Latte Bar in East Clock Town after 10PM. Then talk to the guy behind the counter and ask to have a drink, then choose Chateau Romani. It costs 200 rupees.
As always, if you want to have as much time as possible in this dungeon, you should play the Song of Time to go back to the first day, then play the Song of Inverted Time (i.e. play the Song of Time backward) to slow the flow of time, then warp back here.
Gain Access to the Tower
Warp to the Stone Tower owl statue. You have to put three statues on the three switches here, but you have to do so in a specific order or you won't be able to enter the dungeon.
To put the statues on the switches in the correct order, turn so you are facing the Stone Tower. Put a statue on the switch on the right. Then put a statue on the switch on the left. Finally, put a statue on the button closest to the Stone Tower entrance. Then jump across the platforms and go into the Stone Tower.
Get a Stray Fairy
In the first room, there are a couple of Dragonflies, and a Real Bombchu in the middle. Shoot the diamond eye switch on the stone face across from the dungeon entrance. A chest will appear. Use the hookshot on the chest, and open it to get a Stray Fairy.
Get a Second Stray Fairy
Now go through the door on the left side of the entrance. It has a fence next to it.
This room has a few Real Bombchus in it. There are a few normal-sized switches in this room. Put a human Link statue on one of the switches using the Elegy of Emptiness. Find the huge switch and put a Goron Link statue on it.
Now find the cracked wall in this room (across from the door that you entered through) and bomb it. Then break the large crates to find a couple of small crates. Carry a small crate over to one of the remaining small switches and put the crate on it. Do the same for the other remaining switch (or just put a statue on it with Elegy of Emptiness). This will open a gate in the corner of the room. Go past that gate.
There is a Dragonfly in this area and a couple of Guays. The floor has two darker squares in it. One of the squares has grass growing on it, and the other doesn't. Bomb the one that doesn't. As a Goron, roll into the hole that opens up. (If you just fall in, you will be injured when you land.)
You land in a beam of light that is shining down into this dark room. Look at the ceiling to see a Hookshot target. Hit it with the Hookshot and open the chest up there to get a Stray Fairy.
Get the Map
Stand in the light and look at the lava. There is a Sun Block there. Shine light on the Sun Block using your shield Now transform into a Goron. The lava won't hurt you while you're in Goron form. so walk across to the little area past the lava. There is a chest in here that contains the Dungeon Map.
Get a Key
Touch an Armos Statue in the small room where you got the Dungeon Map. It will come to life. You can kill it with a Goron Punch, but it explodes afterward, so press R to shield yourself. Kill the Armos Statues near the Dungeon Map chest and kill the two Armos Statues in the lava. After you kill them, a chest will appear. It contains a Small Key.
Get a Second Key
Go into the passageway near the beam of light to go back upstairs. You will be in the room where you bombed the floor. There is a locked door here. Use your key on it to go through.
Wear the Zora Mask and swim through the pool, under the bridge. Swim to the far side, then remove the Zora Mask. Wait until you have risen up to the surface of the water, then put the Zora Mask back on. Push toward the ledge in front of you before you fall into the water as Zora Link. You should grab onto the ledge before falling. I call this the Zora Mask Trick. Climb up and open the chest here to get another Small Key.
Get the Compass
Kill the Dexihand, then go into the passage underneath where it was. In the next room, press B to dive to the bottom. Walk over to the three floating mines and hold the Z button while you press R. This will allow you to make the mines explode without getting hurt. Step on the switch that was behind the mines. This makes a chest appear.
Press A to Surface. When you get to the surface of the water, climb onto the bridge in the middle. Go to the end of the bridge where there is a beam of light, a mirror, and a Sun Block. Stand in the beam of light and shine it on the mirror. The mirror absorbs the light for the amount of time that you shine light on it. When you stop shining light on it, the mirror will emit a beam of light for the same amount of time as you shined light on it. So shine light on that mirror for a while, then stand in the beam from the mirror and shine the light onto the Sun Block.
Go past where the Sun Block was and kill the Bombchu there, then open the chest to get the Compass.
Important! If you didn't do this already: before you leave, step on the switch underwater in the south wall of the room to make a chest appear.
Get a Third Stray Fairy
Ignore the door near the chest where you got the Compass. Instead, go back the way that you came. Before you leave, while standing on the bridge in the water in this room, turn around to see a frozen diamond eye switch. Shoot it with a fire arrow to make a chest appear.
Now go to the locked door behind you and go through.
Wear the Stone Mask to keep the Black Boes at bay in this room. Otherwise they keep regenerating.
As a Goron, punch the pillar until it's gone. Then stand in the light and shine the light rightward, on the leftmost sun face. If you shined light at the correct one, a chest appears near the pillar in the middle of the room. Open it to get a Stray Fairy.
Get a Fourth Stray Fairy
Now shine light on the right-hand mirror in the middle. As mentioned before, the mirror will shoot a beam of light for the same amount of time that you shined light into it, so shine light into it for a while, then stand in the beam of light that it shoots out and shine it onto the Sun Block on the right. Do the same to shine light on the Sun Block in the back of the room.
Go into the path that you opened to the right. There is a chest at the end of the path that contains a Stray Fairy.
Get a Fifth Stray Fairy
Now go through the door past the Sun Block in the back of the room.
First, become a Goron, then go down to the lava below. Ground Pound the switch in the lava. Then slowly roll around the lava to the left and step on the switch at the end before the flames come up again. The trick is to roll slowly. If you roll slowly enough, you won't bounce off of walls so much, so there will be fewer delays. After you press that switch, the flames disappear around a chest up above. The flames will not reappear around the chest.
Go back around the lava and climb up the ladder at the end. Become Deku Link and get into the flower. Go up and float forward to the air flow up ahead. When the air blows you upward, turn to the left and land in the area with rupees and a chest. It can be difficult to turn while floating, so if necessary, float backward to get back into the air flow. When you reach the ledge with the rupees and chest, open the chest to get a Stray Fairy.
Get a Sixth Stray Fairy
From the ledge where there were rupees and a Stray Fairy chest, roll as a Goron down to the lava below. Climb up the ladder to the right.
Use the Deku Flower again to float forward into the air flow straight ahead. From there, carefully turn toward the left in order to use the next air vent. If you aren't able to change direction, float backward toward the air flow and try again. After the second vent, you pass some rails that have a Bombchu on them. Don't get close to the Bombchu. Float to the air vent after those rails, then keep going straight and land on the ledge in front of you. Open the chest (see the previous section if there are flames around the chest) to get a Stray Fairy.
Mini-Boss: Garo Master
Go into the door across from the aforementioned Stray Fairy chest.
Garo Master attacks. He will charge toward you with his flaming sabers. Sidestep when he charges, then hit him while he stands there looking for you. Shield yourself as soon as you hit him so you can block his counterattack. If he disappears, run away because he is about to fall from the ceiling. You can try to do a Ground Pound as a Goron the moment that the Garo Master is about to hit you with his charge attack, then punch him if you didn't hit him with the Ground Pound. You can also stun Garo Master with the Hookshot or Deku Nuts.
Get the Light Arrows
Open the chest that appeared after you defeated Garo Master. You get the Light Arrows. Note that some enemies, such as Guays and Blue Bubbles, will drop 50 rupees if you shoot them with Light Arrows.
Get a Seventh Stray Fairy
From the room where you got the Light Arrows, exit the room through the door that has a symbol above it.
Climb up onto the metal thing directly in front of the door. Run off of the end of it, onto the stone bridge. Use the Hookshot or bombs to get rid of the Hiploop's mask, then kill it. If you fall down to the bottom of this room, use the hookshot on the target on the ceiling above the door that you entered through. After you get rid of the Hiploop on the bridge, go through the door beyond it.
Go forward until the Eyegore wakes up and starts moving. Stay close to it until it starts moving to make an attack, then back up and shoot it with a Light Arrow while its eye is yellow. Repeat this until it dies. After it dies, open the chest that appeared and you will get a Stray Fairy.
Change the Layout
Go out of the door past the Eyegore. You will be back in the first room of the dungeon. Go through the door in the south wall to exit the dungeon. (You have to leave the dungeon to continue.)
Go to the right and step on the switch. The middle block will move, revealing a red jewel. Play the Elegy of Emptiness to leave a statue on the switch. Then stand on one of the platforms next to the red jewel that you just revealed on the wall in front of the dungeon. Stand on the inner far corner of that platform and turn around and shoot the red jewel with a Light Arrow. If you are all out of magic power, play the Song of Soaring and warp to the Stone Tower. Break the jars on this side to replenish your magic. Then step on the left switch and play the Elegy of Emptiness, then stand to the side and shoot the red jewel from there.
Get a Eighth Stray Fairy
Jump across the blocks to get back into the temple. Walk straight ahead so you are standing on the gray symbol on the floor. Turn around and look up, then shoot a Light Arrow at the sun symbol on the wall up above. A chest appears in front of you. Go around to the front of it and open it to get another Stray Fairy.
Get a Third Key
Now go into the eastern door. Shoot the Sun Block with a Light Arrow to make it go away. Go past where it was and put on the Deku Mask. Use the flower up ahead to float into one of the air vents, then use it to float onto the bridge in the middle. Use the Hookshot or bombs to get rid of the Hiploop's mask, then kill it. Turn around and shoot the sun face with a Light Arrow.
Then go through the passage at the end of the bridge that the Hiploop was on. Step on the switch, then go back the way that you came and open the chest that appeared. You get another small key.
Get a Ninth Stray Fairy
In the same room as the Hiploop on the bridge and the small key, if you didn't shoot a frozen diamond eye earlier in the dungeon, then go to the end of the bridge across from the small key chest, and fall off the bridge there. You land on a ledge above the three air vents. Turn around and use a Fire Arrow on the frozen diamond eye switch on the wall. Then as a Deku Scrub, walk into the middle air vent and float toward the chest that just appeared. The chest can be accessed by falling into the middle air vent as a Deku Scrub and floating to the chest under the bridge, across from the diamond eye switch. Open the chest to get a Stray Fairy.
Get a Tenth Stray Fairy
Use an air vent to float up to the ledge on east wall. Take off the Deku Mask and step on the switch there, then use the hookshot on the chest that where the flames went away. If that chest isn't there, you have to flip the dungeon right-side-up, then go to where you got the compass (the room east of the entrance), and step on the switch underwater that is surrounded by mines along the south wall. Then go out and flip the dungeon upside-down again, and remove the flames as described earlier. Float to the farthest air vent from the switch that you stepped on to remove the flames. Use it to float up to the chest that you unblocked from the flames.
Reach the Next Mini-Boss
As a Deku Scrub, use the air vent to fly to the high corner of the room where there is a platform. Go through the locked door there.
Shoot a Light Arrow at the red jewel on the wall across the way. Become a Goron and go across the lava, then take off the Goron Mask and shoot a Light Arrow at the jewel again so you can go through the door.
In the next room, you can kill the ChuChus to get more arrows and magic. The ChuChus will reappear over and over.
Hit the red jewel with a Light Arrow to flip the room, then move the stone block to the middle of its area. Flip the room again. Pull or push the block between the two ramps until it falls to the lower area. Flip the room again. Push the block until it's touching the raised floor in the corner. Flip the room again. Push the block into the hole with the symbol on it. The door will open. Climb up onto the stone block that you pushed, then jump from there to the ledge with the door on it. Go through.
Kill Wizzrobe as you have done before, but be careful of the lava that falls from above this time. You should be safe if you don't move from the spot where you first entered the room. Also, the Wizrobe can appear on higher levels, so make sure you look around at all possible spots to find him.
Get an Eleventh Stray Fairy
Use the Hookshot on the chest that appeared. Open it to get another Stray Fairy.
Get a Fourth Key
Go down the stairs near the chest that you just opened. Use arrows to kill the Poe that appears nearby. Then as a Deku Scrub, float across to the other side of the room where there is a door, being careful to avoid the Poes that appear along the way. Don't go through the door on the other side. Instead, kill the two remaining Poes, then as a Deku Scrub, use the flower and float into the passageway to the right of the exit door.
There are a few Death Armos going through these passages. You can kill a Death Armos by first hitting the symbol on its front or back with a Light Arrow, causing it to flip over. Then walk under it to make it crash into the floor, killing it. Or just wear the Stone Mask to make them leave you alone.
Find the switch that is in the south side of the Death Armos area, then step on it and play the Elegy of Emptiness to keep the switch pressed. Go to the chest to the left and open it to get a Small Key.
Reach the Third Mini-Boss
Go back to where you came from and land on the platform with the Deku Flower. Go through the door.
Shoot at the mines that are in front and slightly to the left. This will make a couple of them explode. Use the Deku Flower here and float past where those mines were. In this alcove, the pots will attack you, so raise your shield. Then use the Deku Flower to float to the left, where there is a door. Go through.
Kill the Bubbles here. If you get hit and become jinxed, play the Song of Storms to cure yourself, or just wait for exactly one minute, when the jinx wears off. Go into the door at the end.
Keep your shield raised. Shoot Gomess with a Light Arrow to get the bats to fly away, then run up and hit the orb in Gomess's body with your sword. Quickly raise your shield to defend against the counterattack after you hit the orb. If you run low on magic or arrows, become Zora Link and press R and B to use your electric barrier while touching the bats to kill them, then collect the items that fall. But be sure to do that before your magic becomes empty. Otherwise, you will need to try to kill the bats by other means.
Get the Boss Key
Go into the door that opened. Open the chest to get the Boss Key.
Nintendo 64 Version: Get the Giant's Mask
If you are playing the original Nintendo 64 version, you can get the Giant's Mask here. If you are playing the Nintendo 3DS version, you will get the mask later. Go back the way that you came, through the room with the blue Bubbles, until you reach a Deku Flower. First, shoot the mines on the right to make a couple of them explode. Then use the Deku Flower to float past where the mines were. Then use the Deku Flower to float to the right again. From there, turn left and walk across the narrow ledge to reach the southwest door. Go through.
You're back in the first room of the dungeon. Put on the Stone Mask and jump across to the platform with the Death Armos and the switch. You should be able to jump across the gap without falling in. Step on the switch. A chest appears on the ceiling. You can Z-Target it. Use the Hookshot on it to be pulled up above. Walk across the short bridge here, then open the locked door.
This is another Eyegore. This one shoots lasers. Shoot it with a Light Arrow, then shoot a regular arrow at its eye. Repeat the process until it dies. After it dies, open the chest to get the Giant's Mask.
Get a Twelfth Stray Fairy
Go through the door behind where the Eyegore was. Walk past the spiked roller and hit the crystal switch. This makes a chest appear on the ceiling. It contains a Stray Fairy, but you will have to flip the dungeon before you can access it.
You can reach the boss door now, but first this walkthrough will explain how to get the rest of the Stray Fairies.
First, play the Song of Soaring to warp to the entrance of the dungeon. Leave the dungeon. Outside, play the Song of Soaring and warp to the Stone Tower. This causes the dungeon to flip back over to be right-side-up. From the Stone Tower owl statue, turn to face the dungeon, then put a statue on the right switch with the Elegy of Emptiness. Then put a statue on the left switch, and finally on the switch closest to the dungeon. Jump over the platforms and enter the right-side-up dungeon.
Fall down into the pit and open the chest on the floor. It contains a Stray Fairy.
Get a Thirteenth Stray Fairy
Go up the ladder to get out of the pit, and go to the right. Go through the door that is near the fence.
Complete the puzzle in here once again: put a statue or two on the normal-sized switches with the Elegy of Emptiness. Put a Goron Statue on the huge switch. Then break the big crates and put a small crate or two onto the final switch or switches. Go through the gate that opened. Go straight ahead and go into the door on the right.
You will be back in the water room. Use a Light Arrow on the Sun Block to the left. Then get in the water as a Zora and swim to the far side. Do the Zora Mask Trick to reach the ledge there. The Zora Mask Trick is: while facing the ledge with a chest on it, take off the Zora Mask. Wait until you have risen up to the surface of the water, then put the Zora Mask on. Push toward the ledge so that you pull yourself up onto the ledge before you fall into the water.
While standing on this ledge, you can do a sword spin attack to hit the crystal switch through the fence. As a Zora, go back into the water and use the Zora Mask trick as described in the previous paragraph to go up onto the ledge on the opposite side of the room. Throw a bomb at the Beamos to kill it. Then open the chest that appeared when you hit the crystal switch, and you will get a Stray Fairy.
Get a Fourteenth Stray Fairy
Swim into the water and go under the bridge. Swim into the passageway under the Dexihand. In the next room, swim straight ahead to find a chest on a small platform. Open it to get another Stray Fairy.
Get a Fifteenth Stray Fairy
In the same room, swim to the surface of the water and go up onto the bridge in the middle. Go through the door in the north wall. In this room with the mirrors, go through the door in the north wall. Fall down to the lava area and walk along the ledge around the edge of the room. When you can see the third air vent, look up to see a sun face on the wall. Shoot it with a Light Arrow and go up the ladder that appears. Go through the door there. You will be back where you fight the Garo Master. Go through the door on the left. Fall down below and open the chest there to get the final Stray Fairy.
Go to the Dungeon Boss
The dungeon needs to be upside-down for you to reach the boss, so go outside by playing the Song of Soaring and go out from the entrance. Put a statue on the switch to the right, then stand on the inner corner of one of the platforms in front of the dungeon entrance. Turn around and shoot a Light Arrow at the red jewel. Then jump over the platforms and enter the upside-down dungeon.
In the entrance room, target the treasure chest on the ceiling, and use the Hookshot on it. You might need to move around to find a spot where the hookshot can reach the chest. Up there, walk across the small bridge and go into the door at the end. In the next room, go past the open chest and go straight ahead through the door at the end. In the next room, there is another treasure chest on the ceiling that you can target. Use the hookshot on it. Then use the hookshot on a ceiling target up ahead. The Boss Door is straight ahead, but if you need to replenish your magic, there are some pots across from the boss door that you can reach after you kill the Beamos with a bomb. When you're ready, go through the boss door.
You will be in the same room where you fought Garo Master, but upside-down. Fall into the hole in the middle of the room.
Be careful not to fall off of the edge in this battle. If you do, you have to start the battle over again. Unfortunately, you can't actually see the edge until it's too late, but as long as you don't go too far away from the rocks and stones, you will remain within the battle area.
Twinmold's tail segments are their vulnerable spots.
The best strategy is to attack Twinmold's tails while wearing the Giant's Mask. If you are playing the Nintendo 64 version, you got the mask earlier in the dungeon by defeating the second Eyegore. In the Nintendo 3DS version, you get the Giant's Mask during this boss battle after shooting out the eyes on Twinmold's underside, then shooting the tail eye.
Unfortunately, the Giant's Mask drains magic very quickly. But if you drank a bottle of Chateau Romani as recommended, your magic meter won't deplete, leaving you free to wear the Giant's Mask throughout the entire battle. If you do that, you can just hack and slash Twinmold's tails until they die.
You can get more magic if you break the stone structures as a giant, but the giant can't collect the power-ups, so be sure to quickly take off the Giant's Mask and put on the Bunny Hood to run over and collect the power-ups.
Otherwise, you can hit Twinmold's tails with Light Arrows, or if you have no magic at all, try running up close to Twinmold and hit the tail segment with the sword, or Fire Punches, or Bombs or the Blast Mask.
After the battle, get the Heart Container, then step into the light to get Twinmold's Remains.
Great Fairy Fountain
Don't play the Song of Time yet! If you collected all of the Stray Fairies, be sure to go to the Great Fairy Fountain, which you can reach in the same area as the Music Box House. The entrance is to the right of the stone face in the wall that leads to the Stone Tower. From where you end up after the Twinmold battle, fall down the ledge to the right and go into the door in the jar-shaped house. The Great Fairy of Kindness will give you the Great Fairy Sword. It's the strongest sword in the game, but it's an item, and it is a two-handed sword, so you can't use your shield at the same time.
Prepare for the Clock Tower
Now that you have defeated all four of the dungeon bosses, you can reach the final boss. However, you might want to prepare first. You can access most of the Pieces of Heart, and you might want to pick up any Masks that you haven't collected yet. If you collect all of the masks before the next part of the game, you get a very helpful bonus.
When you are ready, go to the night of the Final Day and wait at the Clock Tower until midnight. Then climb the tower and go on top. Play the Oath to Order as soon as you can. You will see a cut scene involving the Moon.