Be sure to get refills of green potion and fairies; you'll need them in Ganon's Tower. To get back to the Tower you will need to use the Turtle Rock transporter in the Light World.
From Turtle Rock, head west. You'll encounter Lynels on the way; they can only be hurt by the blade of your sword, and not by sword beams. Watch out for the fireball they spit, and kill them. When you reach Ganon's Tower, stand in front of it and the crystals will float up and break the barrier. Stairs will be revealed; go up them into the Tower.
Get down off the ledge and head to the northeast corner of the room, where there are stairs leading down. Go down them, and in the next room, don't pull the lever or bombs will fall from above. The chests just contain arrows and bombs. Pick up the bottom-left skull to uncover a switch that won't stay down. Use the Cane of Somaria to make a block to push onto it, then go through the east door.
Stand in the doorway until the swirly thing hits the doorframe, then quickly step out so the Wallmaster doesn't catch you. Keep moving so you avoid tiles, Bubble, and Wallmaster alike. Leave the Bubble until the tiles stop flying, then use Magic Powder on it to turn it to a fairy and replenish the health you probably lost. When the tiles are gone and the Wallmaster goes back to the ceiling, a small chest will appear. Open it for a small key and exit east through the locked door.
Kill the Gibdo and go east to the two blocks. Push the lower block down. Pick up the two skulls (one hides a large magic jar), then go to the bottom of the room, past the spike trap, and kill the two blue Bari, avoiding the fireballs. You will have to light all four torches in here with the Fire Rod to open the south door. Make sure to be careful of the Wallmaster as you go. Go to the top of the room, light the torch, then go down and across the conveyor belt and light the torch below the blocks, then get past the spike trap and go to the bottom of the room and light the two torches here. Exit south.
Kill all the Gibdo in here (lure the far one by standing against the south wall). Then you must throw a bomb onto the conveyor belt so it explodes on the crystal switch. Stand at the very top of the small wall, drop the bomb, then pick it up with A and throw it (do it fast or the bomb will explode too soon). The blue blocks will go down. Then do it again; throw another bomb to explode on the switch, and run past the blue line so you'll be on the other side when the blue blocks go up. When the orange blocks are down, lift the skulls for a small magic jar and a bomb. Exit west.
Kill the Hardhat Beetles, then open all but the upper-left chest for some rupees and arrows. Now open the upper-left chest for the compass, and a bunch of holes will appear around the room. Step onto the orange warp tile.
Kill the blue Bari and go against the conveyor belt to the stars at the end then STOP or you will fall into the hole that appears to the right. Let the conveyor belt below take you to the next stars, and once the holes change pick up the skulls above for a small key. Run across the next conveyor belt onto the stars and STOP again, because a hole appears right in front of you again. Go across the lower conveyor, killing the Bari, and go through the locked door.
Quickly put on the Magic Cape and dash south along the bridge (which will collapse from below in a few moments), then lift the skull to the right and take off the Magic Cape, killing the Hardhat Beetle. Exit through the door to the west.
Kill the Hardhat Beetle on the island if you can, then go around and pull the statue down to reveal a star. Move the statue aside and step on the star, then go around down the bridge that appeared and step on the warp tile.
There's an invisible floor that goes straight west, so you don't even need to light the torch (which illuminates the path); just head west and through the door to the next room.
Go west then north to the top of the room (hint: lift the top skull). Kill any Hardhat Beetles you can. Go near the door above, but don't go through. Walk to the right edge next to the door and you see a torch. When you light it with the Fire Rod, an invisible path is illuminated. If you lifted the top skull, you can use the hookshot on the lower one to quickly get across so you can make your way along the now-illuminated path and reach the door at the end. If the torch goes out before you get across, either use Ether to light the path for a second, or use the Cane of Somaria and push blocks off edges as described earlier until you find your way. If you used your hookshot to get to the path, you should have plenty of time. Go through the door at the end of the invisible path.
Use Magic Powder on the Bubbles to get them out of the way. The chest just contains arrows. Bomb the bottom-right cracked floor to open a hole. Drop into it to encounter a mini-boss, the Armos Knights. It's the same as before, but the floor is icy, so it's a little trickier. The Knights will fall with just one silver Arrow. Kill them, then exit north for three chests containing the Big Key, arrows, and bombs. Go back to the Armos Knights' room and exit west.
If you need fairies, dash into the crack in the north wall to open it (watch for the black scurrying monsters again), and there are four fairies there. Go back out and up the stairs.
Push aside the block to the right and open the Big Chest for the Red Mail! Damage is cut in half again. Red tunic, purple hat, green sleeves. Lovely. Exit north from the Big Chest room, then up the stairs (ignoring the small key on the lamp, unless you want to go around this floor looking for the map, which you shouldn't need following this walkthrough), and now go up the center stairs in the north wall.
This spiky-floored room has blue and orange blocks, as well as Goriyas mimicking your movements. Remember, the red one spits fire. Go down and use Magic Powder on the Bubble to get rid of it. Hit the top-right crystal switch to lower the blue blocks, then make your way along the blue lines down near the door. Walk up the blue line towards the crystal switch, pick up the skull and throw it to hit the switch. Go west to where there are two blocks, and push the top one up to open the door. Then go back along the orange line to the center of the room, then up to the skull below the crystal switch. Pick it up and stand in the center were another skull was, throw the skull at the switch, and step back so you don't get caught on the orange blocks. The blue blocks should be down, allowing you to exit south.
This room is simple. Grab hold of the statue (or better yet, the wall below you), and move the controller to make the red Goriyas come to you, where you should kill them with arrows as you have in the past (from the side, to avoid their fireball). Once both Goriyas are dead, the door opens; go through.
In here you must kill the red Goriyas while avoiding the Beamos's beams. (The skulls hide nothing important.) Do your best and exit through the north door, and from there go north along this corridor through the Big Key door. Go through.
Go up around the upper path until you reach a ledge you can drop down above the spike trap. Go down below, then walk right up to the crystal switch and hit it, freeing a spike trap directly below you. Go north, awakening the Eyegore Statues, and kill them with arrows. You have to do it carefully because you can't see when they wake up. Walk up close to one from below, then quickly retreat, turn around, and fire an arrow. That should kill them. Then pick up the center pot above and step on the switch to open the door. In the gauntlet of spike traps below, try to hit the crystal switch such that most of the traps are trapped at the sides, so you can go south safely and up the stairs. Once above, exit at the top-right.
Carefully cross the bridge, avoiding the black blobs coming from both sides. Go up the stairs.
In the next several rooms, your goal is to defeat all the enemies to open the next door, while avoiding the beams from the Beamos. Once you reach the room where most of the floor is covered by ice and the Beamos is stationary, you're best off using Bombos to kill all the enemies on the screen, then rush for the door, avoiding the fireballs and Beamos's beam. In the corridor with the yellow swirly thing, stand behind a statue to avoid letting it touch you. Go west and you reach a sand-filled room where the desert Lanmolas attack. Beat them as before (your sword beams can hurt them from afar), though be careful of the fireball-spewing statue in the corner. Once they're gone, exit north, where the four skulls hide a few recovery items. Go up the stairs.
Normally I do not recommend using Ether to reveal an invisible path, but in this instance, wait for the Skull Wizzrobes to appear, then use Ether to kill all three and open the door, watching the floor for the path out of here. If you can't remember the way, use the Cane of Somaria to create blocks and push them off the edges. Exit through the south door.
Dash east to get past the laser eyes, and exit north. Defeat the Skull Wizzrobes one by one, avoiding the spike trap and being careful of the moving floor. When you've killed them all, exit north.
Quickly dash north before the path crumbles. You'll bust your way through some red Tauruses. Exit east to the next room.
Careful of the spinning flame, lift the three skulls that are blocking the torches, then go back west to safety before attempting ot light them. Following the spinning flame, use the Fire Rod to light the top, right, bottom, and finally left torch to open the door. The skull closest to the door hides a small magic jar. Exit east.
Avoid the lasers from the eyes and make your way to the top of the room (holding B to keep your shield to the right). Get the heart and full magic jar from the skulls. Then face north, hold B, and go backwards to get to the stairs leading up.
The floor in this room will collapse so you have to be quick to light those torches. Run right, light the bottom-right torch, run left, light the bottom-left torch, then run up and light the top two torches and run through the exit.
Throw skulls at the Hiploops for a small key, avoiding the fireballs. The chests just contain bombs. Exit west through the locked door.
Stand at the far left above the conveyor and throw a bomb onto it so it explodes in front of the crack. Bait the giant spike trap and carefully go through the hole.
Wait a moment for the yellow swirly thing to hit the barrier and disappear. Then hit a crystal switch, watching out for the fireball. Use Magic Powder on the Bubble to turn it into a fairy. The bottom-right skull hides a large magic jar. Get inside the orange lines and hit a crystal switch so you can reach the chest inside for a small key. Then exit through the locked door below.
Now you must face Moldorm again. It's the same as before, but your battlefield is a bit larger. There are still plenty of places to fall below, so try not to fall! If you fall, you land in a huge room with Skull Wizzrobes and a red Bubble, and there's a staircase in the northeaast corner that takes you back to Moldorm's room. Luckily, it takes a mere two hits from the Golden Sword to kill Moldorm. Once you've killed Moldorm, a chest appears to the south. Hookshot across to it; it just holds 20 rupees. Go up the stairs, push the top block left, the bottom block left, and the top block left to get out. Exit west.
Go straight down to the line of ice below you and wait for the Hiploop to approach. Kill it with a silver arrow. Then go north near the blue bouncy things and activate your Magic Cape. Make your way north, straight up through the center of the room. Take off the cape at the stairs and go up the stairs.
This is the final corridor before you meet this dungeon's boss. Ganon? Let's find out. Go west along the path to reach the boss door. Inside, it's...
-- Agahnim II --
Agahnim? But where's Ganon..? After a little chit-chat, Agahnim splits into three, with two clones of himself and one real Agahnim. Only the real one can be harmed; it's the one with the darkest shadow. Agahnim doesn't do the lightning attack this time around, so don't worry about that. Each time the clones move, get in a good position so that you will hit the real Agahnim. Remember that they will all turn to face your direction. Sidestep around the circles of blue orbs that break apart on contact, and knock the flashing orbs back at the real Agahnim (energy orbs will simply go right through the clones).
After you hit the real one 6 times, the clones return to Agahnim's body, Agahnim collapses to the floor, and Ganon's evil spirit rises from his body! Yikes! It turns into a blue bat, and you see it fly out of the tower. You automatically play your flute, and somehow the bird from the Light World comes flying in and picks you up to follow Ganon.
You will see the bat fly from Ganon's Tower to the Pyramid of Power, where it will crash through the top, creating a large hole. The bird will set you down right in front of it.
The final battle is nigh. You are going to want three fairies, and one bottleful of green potion. You may also want red potion, but be sure to bring at least one fairy. You NEED the silver arrows for the next fight (they're the only things that can kill Ganon), and the Golden Sword is a must, so if you haven't visited the Fat Fairy yet, go back to the "Fat Fairy" section to find out how to reach her. You'll really want all of your upgrades before the fight begins.
If you're ready, fall down the hole in the top of the Pyramid of Power to face the King of Darkness!
-- Ganon --
At the start of the battle, the hulking, pig-like Ganon will throw his trident around the room, and will also teleport from one place to another. It's easy enough to avoid the trident; just watch where Ganon and the trident are moving so you can attack him again. After a while, Ganon will create a circle of fireballs around him that expands, so stay far away to avoid getting hit. The fireballs turn into fire bats that will fly at you; they fly in straight lines at you, so sidestep them carefully. Continue hitting Ganon with the Golden Sword (he is easier to hit when he is at the top of the room; the fireballs will probably form near where you're trying to hit him from above). As soon as you see Ganon stop using his trident, hit him as soon as you can or he will cause a fire bat to swirl around him, leaving flames. If you're not quick enough to prevent him from creating the flame bat, run away, but not at an edge of the room. He will pound the ground, causing one edge of the perimiter tiles to fall. If you fall down below, you will have to leave the Pyramid and start the battle over. Once all four of the edges of the floor have crumbled away, Ganon will start shooting a line of fire at you as he teleports. Then the room turns dark and Ganon becomes invisible. You must light the torches in the corners to make Ganon visible and vulnerable again. Once the room is lit, hit him with the Golden Sword to stun him, then shoot him with a Silver Arrow. Repeat this process, and after shooting him for the third or fourth time, he explodes, utterly destroyed!
The door above opens, and a beautiful golden light flows forth. Go inside to find the Essence of the Triforce.
You've done it. You have destroyed the evil King of Darkness, and the Triforce is in your righteous hands. Watch the ending scenes to see the fulfillment of Link's heart's wish. Congratulations!