The Stone Tower is a large and deep dungeon. Unlike the previous three dungeons, which focused mostly on one form of Link, you'll have to use all the forms together here to get through.
To the first mini-boss
The entrance room isn't too interesting, so go through the left door. In this room, there are four switches that all need to be pressed at once to make the gate to the next area open. The big switch's meant for the Goron, the other two are for Human and Zora Link, but how do you depress the fourth switch? The answer's simple: look around to find a cracked wall and bomb it to discover a few small crates hidden behind a row of large ones. Pick them up and place them on the switches to keep them held, allowing you to get through to the next area.
In here, the dark area on the floor that doesn't have grass growing on it is meant to be bombed. Drop down the hole (it's a long way down so it's best to use the Goron to roll down) and use the Mirror Shield to deflect light onto the sun block to make it disappear. Roll across as a Goron and open the chest to get the Dungeon Map. Afterwards, kill the Armos Statues beside the chest and inside the lava (they're hurt by Goron Link's punch) to make a treasure chest appear containing a Small Key.
Go upstairs and use your key on the locked door. Put on the Zora Mask, jump into the pool and swim across, where you'll see a Dexihand. Don't kill it! Let yourself be grabbed by it and it will throw you upwards. Open the chest you see here to get another Small Key. Or if that doesn't work for you, then kill the dexihand, line yourself up with the platform that has the switch on it, and jump from the water (press "A" and surface while pressing "R") onto it. Afterwards, jump back into the pool and swim through the passage below the Dexihand.
Once through the passage, surface and climb out of the pool. Here there's a source of light and a sun block. To reach it, first shine the light into the nearby mirror for a few seconds, which will cause the mirror to start shining for a short period. Run over and deflect the light to the sun block to make it disappear. In the small alcove that is uncovered in the process, you'll find the Compass. The door you see leads back to the entrance, so go the other way and open the locked door.
The Black Boes in this room will generate indefinitely, so don't bother trying to kill them all. You can wear the stone mask to stop them from coming back, if they are a problem. First, put on the Goron Mask and punch the pillar to uncover a source of light. You'll need to use the mirrors to get rid of the sun block on the opposite side. First deflect light to one of the center mirrors for a while, then run across and deflect the light to the mirror on the wall. From here, deflect the light onto the sun block to make it disappear, allowing you to get through.
In this room, there are several airstreams that will allow Deku Link to get across to the other side, that is if you manage to hit them all. If you don't, you'll fall into the lava and have to restart. This isn't as easy as it seems because of the difficult controls, and it may take a few tries. Once on the other side, go through the door to meet your first mini-boss...
Mini-boss 1: Garo Master
This mini-boss is hard if you don't know what you're doing. He has two attacks: in the first, he simply rushes into you with his flaming swords. However, and this is his second attack, sometimes he disappears before reaching you, only to ambush you from behind seconds later, so be prepared for this attack.
If you block his attack he will immediately stand up. You only have a chance to reach him if you dodge his attack, which will render him confused for a short while. Use this opportunity to strike, and immediately get your shield up to prepare against his counterattack. An easy way to do is is to simply put on the Goron Mask and do a Goron Pound as he attacks, which will dodge his attack and allow you to punch him right away if the pound didn't already hit.
Once he is dead, he will tell you about the red switches. To be able to use them, open the chest that appears to get the Light Arrows!
To the second mini-boss
In the next room, jump across to the platform with the masked Hiploop. To get rid of his protective mask, either use the Hookshot or bombs, afterwards kill him any way you like. Get through the door to enjoy your first Eyegore fight. To kill these, avoid his attack, and shoot his eye with a Light Arrow as it turns yellow. Go through the door to end up back at the entrance and exit the temple. (Yes, that is right.)
Once outside, step on the right switch and play the Elegy of Emptiness to remove the middle block. Walk on top of one of the other blocks to notice the red switch. Shoot a Light Arrow at it and everything will turn upside down, causing you to fall to the sky...
The blocks are already placed for you, so jump across to get back into the temple. Walk across to the right door and enter it. Use a light arrow to get rid of the sun block. In here, put on the Deku Mask and use the airstreams to get up onto the bridge where another masked Hiploop awaits. Go through the passage and step on the switch in the middle to make a chest appear back in the room, then run back and open the chest to get a Small Key. Now, jump into the airstream to fly all the way up to the northwest corner and go through the locked door.
Here, shoot the red switch to flip the room, roll across the lava as a Goron and shoot the red switch again to turn the room back so you can go through the door. The next room has a small puzzle, where you need to move the block across to the small depression in the ground by flipping the room repeatedly. There are Chuchus here to refill your magic and arrows should you run out, and the puzzle is very straightforward. Once you've done that, the door will unlock allowing you to go through.
Mini-boss 2: Wizzrobe (4)
Yep, it's him again. This time, it's a bit more annoying because of the lava that drops from the ceiling and hurts you, but ultimately the whole thing works just the same. Once he's dead, Hookshot the chest that appears and go downstairs.
To the third mini-boss
Once there you'll need to fly to the other side, which is a bit difficult due to the Poes. Try to avoid them and get across. Once there, fly up to the southern passage you see to your right. This area is littered with Death Armos which are an extreme pain, if you have the Stone Mask use it to get through safely. On the other side, step on the switch and play the Elegy of Emptiness, then get to the chest to acquire a Small Key. Return to the Poe room and go through the door to get to the next area.
Here, shoot one of the mines to open up a path to the left alcove, then fly in using the Deku Flower. From here, fly to the other side of the room and go through the door. Here, kill the Blue Bubbles, go across and enter the door...
Mini-boss 3: Gomess
This guy protects himself using a bunch of bats that fly around him and that he can send after you if you run away. If you get close to him he will also use his scythe to slash you. Shoot a light arrow to get rid of the bat defense, then strike his heart (best to jump attack it) and get back. Repeat this procedure a few times and he will die.
Go into the small side room and open the chest to get the Big Key. Return the way you came from.
To the boss
Go back to the mine room. Fly across and this time take the other door in the southwest corner. You're now back in the entrance room in a solitary corner. Jump across and step on the switch to make a chest appear on the ceiling. Hookshot this chest to get up to the top path and open the locked door. You're now facing another Eyegore, except this time it shoots powerful energy beams. You can defeat it like the last one, or stun it with a Light Arrow and then shoot a regular one into his eye. Once it's defeated, open the chest that appears to get the Giant's Mask! Go across to the next room to continue.
Here, hit the crystal switch to make a chest appear on the ceiling. Hookshot it to get on top of the structure, then hookshot the target in front of you. Now simply jump down and go through the boss door...
Once you're ready, jump into the sandpit to end up in the boss arena. Twinmold is essentially two giant snakes that move around the arena and try to hurt you. Their only vulnerable spots are the tail and the head, which is what you'll want to hit. (Arguably, hitting the tail is much easier.)
If you have the Giant's Mask, this fight is easy. Put it on and strike the tails with your sword. Since the Giant's Mask takes a lot of magic power, destroy the pillars to get some magic refills (you'll have to take off the mask to collect them), or just use a Chateau Romani which makes the whole thing super easy.
If you don't have it, stand on the central platform, because the sand makes you sink down to your death. One little known fact is that the two snakes have weaknesses: the blue one is weak to Fire Arrows and the red one is weak to Ice Arrows. Use this knowledge to hit their tails. (If you run out of arrows or magic, you can lure Twinmold to the pillars to have them destroy the pillars for you.)
Whichever way you choose, the fight is really not hard and the two should be dead soon. Collect the obligatory Heart Container and step into the portal to be taken outside.
Stray Fairy locations
- Entrance room, Shoot the switch on the left eye and open the chest in the middle.
- Western basement room. Hookshot to the ceiling and open the chest.
- Northeast room with disks and mirrors: Chest in the east-side of the central pillar.
- Northeast room with disks and mirrors: Chest behind eastern sun block
- North lava room, use deku flower to reach platform with rupees and open chest.
- North lava room, as Goron, pound the switch in lava, and roll to the switch on the other side before the force field reactivates. As Deku, fly across to the other side.
- In the water room returning from the fight with garo master, kill the Eyegore. A chest will appear.
- In the water room north of the entrance, after getting light arrows and returning, shoot the sun block on the east and hit the crystal switch. Shoot the left sun block and open the chest.
- Inverted entrance room, illuminate the sun icon with light arrow (if not done already) and open the chest.
- Inverted east room, as deku, fly to the right-side of the room and weight down the switch. Fly to the left, and then to the chest on top to get the fairy.
- Inverted east room, Melt the eye switch, and as Deku, fly on the center updraft and reach the lower room doorway. You can't go through, but you can open the chest.
- Inverted lava room containing Wizrobe. Open the chest that appears when you defeat him.
- Upright, entrance room floor after unlocking boss route.
- Upright, south of demi-boss after unlocking boss route. Head via the northern lava room and open the chest on the return trip.
- In inverted east room, shoot the sun icon near on the high southern platform. Return in the upright east room.
When you have all 15 fairies, return to the small building to the right of the Stone Tower. The Great Fairy of Kindness will thank you for your aid and grants you the Great Fairy's Sword. This two handed weapon is the most damaging, but you won't be able to use your shield with it.