Go down the stairs and quickly run past the Beamos so they don't zap you. You reach a central room, with an area in the center shielded by an evil barrier.
To destroy this barrier and progress further into the dungeon, you must get through all six corridors, each a reflection of the six Sages' temples. At the end of each corridor is an orb that powers the central barrier. You must shoot it with a Light Arrow to destroy it.
I'll guide you through the hallways in a counter-clockwise order, starting from the entrance.
If you are running low on health, there is a hidden chamber on the lower floor in the southern wall, below the entrance of the castle. It houses a bunch of fairies, and four Business Scrubs who will sell you green potion, red potion, arrows, and bombs (equip the Hylian Shield, the Mirror Shield will cause their Deku Nuts to break on contact, rather than bounce off). If you're having trouble finding the chamber, use the Lens of Truth.
Kill the Wolfos that attacks (ignore the chest that appears, I think it's a trap), then use Din's Fire to light the torches below. Equip the Fire Arrows and shoot the unlit torch above the exit. Go through the door.
This room requires you to collect silver rupees using the Hover Boots. It can be tricky, so be patient and keep trying.
Play the Song of Time where you enter to create a blue block to your left. Equip the Iron Boots to collect the silver rupee without getting blown away by the fan. Then, while the fan is blowing, equip the Hover Boots and you should land on the platform below the floating rupee. Be sure to bomb the Beamos! Don't worry about the floating rupee yet, instead hover over to the switch near the far wall, and step on it. Put on the Iron Boots and look back to that floating silver rupee you left behind. There is now a longshot target pillar below it, so with Iron Boots equipped, longshot it to get that rupee. Drop down below the pillar, equip the Hover Boots, and hover over to the platform where the Beamos was. From here it is relatively simple to get the remaining three silver rupees. Go through the door that opens.
Break the pots in this room for a magic jar and heart. Shoot the barrier orb with a Light Arrow to destroy it. You will be returned to the central room. Go into the hidden chamber on the lower floor in the south wall if you need to replenish health or items. Then continue counter-clockwise to the Water Hallway (it's down the stairs to the right).
Careful of falling icicles. Ignore all the chests; they are likely to be traps. Kill the two Freezzards, then use your empty bottle (or get rid of a fairy if you have no empty bottles) to catch some blue fire. Use it on the red ice barrier, then bottle some more blue fire, and go through.
You have two minutes to solve the ice block puzzle. First, push the far block to the right, and again to the right so it falls into the hole. Then push the other block over the one that fell into the hole, then left, and left again so it ends up under the ledge. Climb onto the ledge, melt the red ice, and hammer the switch to open the door. Go through.
Break the pots, then shoot the barrier orb with a Light Arrow to be returned to the central hall. Go into the hidden chamber on the lower floor in the south wall if you want to catch another fairy or replenish items. Then go up the stairs to the right of the Water Hallway door to continue to the Shadow Hallway.
Try shooting the green bubble with an arrow to get it out of the way (the green flames can be up when you shoot; you'll still kill it). Then try to shoot the Like Like you can barely see at the center of this dark room.
There is a torch at the right side of the room; light it with a fire arrow. Quickly use the blocks that appear (before they disappear) to get to the center platform, jump across the next white block to get to a further platform with a dark square on it. Use the Lens of Truth to see an invisible path to the left. Walk along it to reach a rusted switch. Hammer it, then return to the platform along the hidden path. Shoot the torch by the unbarred door to create blocks down to a switch to the right. Step on it, then longshot the chest that appears and open it for the Golden Gauntlets! This lets you pick up huge, crescent-marked pillars. Use the Lens of Truth to see a path coming from the right of the platform to the unbarred door. Go through.
Break the pots, shoot the barrier orb with a Light Arrow, and you are returned to the center room, where you can go into the hidden chamber on the lower floor to replenish health and items.
You actually want to leave the dungeon now to get a very helpful upgrade. You can only get it if you have the Golden Gauntlets. Go outside.
Cross the rainbow bridge, turn left, and continue to a huge, crescent-marked pillar. Lift it with A and go into the cave to find a Great Fairy Fountain. Play Zelda's Lullaby, and the fairy will double your defensive power, giving your hearts white outlines. Damage from enemies will be reduced by half. Now return to Ganon's Castle.
Go counter-clockwise from the entrance until you reach the Fire Hallway.
Equip the Goron Tunic right away, as well as the Hover Boots. The central platform will slowly sink into the lava if you aren't wearing the Hover Boots. Wearing them will prevent it from sinking.
Hover to the platform to the right for the first silver rupee, but quickly return to the central platform, because this one is going to fall. Then get the silver rupee from the platform on the left, careful to avoid the spinning flame.
Go further along the central platform until you see a crescent-marked pillar on the left side of the room. Go over to it and lift it with A. You'll throw it behind you, where it will create a platform for another rupee. First collect the one that was under the pillar, return to the center platform, and hover to the platform with the torch slug on it. Grab the rupee, then hover over to the thrown pillar platform to get the final rupee (you may want to take off the Hover Boots once you're on the thrown pillar). Now that you've collected all of the rupees, the door will remain unbarred even if you die. Get to the unbarred door and go through.
Break the pots, shoot the barrier orb with a light arrow, and you are returned to the central room where you can go into the hidden chamber on the lower floor in the south wall to replenish health and items. Continue counter-clockwise from the Fire Hallway door to the Light Hallway. Pick up the pillar to reach it.
There are hidden enemies all around this room. You can just longshot the center of the room to kill the skulltula easily without using the Lens of Truth (Navi shows you where it is). You can also easily pick off the Keese on the chests with arrows; just approach the chests slowly. There are three keese. Ignore all the chests; they either contain trivial items like five rupees, or are traps. Once all the enemies are killed, a chest appears in the middle containing a small key. Grab it and continue to the next room, where you simply play Zelda's Lullaby on the Triforce symbol to get a chest containing another small key. Go through the door.
You have a minute to collect the silver rupees in here. Avoid the rolling boulders to get the two silver rupees in niches along the walls, and two in the central Y-shaped structure. Use the longshot to get the one on top and unbar the door. If you get disoriented, the correct exit to the next room is the one with the symbol above it.
This looks like where the barrier orb should be, but it's empty and a Wallmaster tries to fall on you. Quickly run straight ahead through the fake wall to get to the real Barrier room. Shoot it with a Light Arrow and you are returned to the central room. Replenish health and items in the hidden room on the lower floor in the south wall if you need to. Continue to the last hallway: Spirit.
There are a bunch of razor traps here, so be careful as you collect the silver rupees. It's really not that hard. Bomb the Beamos to get one of the rupees. You will have to pull the Armos statues away from the wall to get the other rupees. I think if you play the Song of Storms in the center of the room, fairies will come out (Navi turns green there).
In the next room, if you spin attack the crystal switch beyond the bars (or just hit it with Biggoron's Sword), it will reveal a chest containing Bombchus. You must use a Bombchu to hit the crystal switch beyond the other set of bars. Aim it so the Bombchu goes through the hole above the bars and hits the switch. If you don't get it right away, keep trying. Once the door is unbarred, proceed to the next area.
Burn the cobwebs in the ceiling with a Fire Arrow, then use the Mirror Shield to aim the sunlight at the sun switch to the right of the arch through which you entered. The other three are traps that cause a Wallmaster to fall from above, so don't shine light on those. Exit to the next room, where you find the barrier orb. Shoot it with a Light Arrow, and you are returned to the central room, where the barrier on the tower is broken. Before proceeding, use the hidden chamber on the lower floor in the south wall to replenish health and items if you need to.
You should probably go to the Business Scrubs and restock on arrows. When you are ready, with at least two fairies in bottles and at least one green or blue potion, cross the bridge into Ganon's Tower.
Quickly shoot down the keese that attack, and kill the rest of the keese from the entrance with arrows. Go up the stairs and you will here someone playing a creepy tune on an organ, which gets louder and louder as you go up...
Kill the Dinalfos that attack in the next room, then continue on, where two Stalfos attack. Open the chest for the Boss Key. Continue to the next room, where two Iron Knuckles sleep. You can wake them both up for a challenge (if you're crazy) or just awaken one at a time and kill them that way.
Leave the pots and climbing wall alone in the next room (you might need the pots later). Just go through the door and continue until you reach...
Run to a corner to avoid getting smashed by Ganondorf's first attack. The floor around the center will collapse, so just the central platform and edges remain. Ganondorf will gradually make the edges collapse as well.
If you ever stay on the central platform too long, Ganondorf will pound it, hurting you severely, so avoid this.
Get out your sword IMMEDIATELY. Ganondorf will throw energy orbs at you. This is just like the Phantom Ganon battle; hit the orb back at him with your sword until it hits him. Once he is hit, shoot him with a Light Arrow (you can't Z-Target in this battle because Navi isn't there), then when he falls below, longshot him to get close so you can slash him repeatedly with your sword. Don't swing too quickly; he is invulnerable for a moment after you hit him. When he recovers, quickly longshot the stained-glass windows in one of the corners to be pulled to safety, and QUICKLY get out your sword again. You want to be holding it when an energy orb comes at you.
If he shoots black energy, wait for him to shoot it out, then run, because it's really hard to deflect it with your sword.
If you ever need a magic refill or anything, climb down to the lower floor and break some pots for recovery items. Try to conserve your green/blue potion and fairies.
Continue with the strategy above until Ganondorf coughs up blood.
The tower will start to collapse and you have three minutes to escape. Follow Zelda as she leads the way to safety. Watch out for falling rocks. At one point Zelda will be trapped in a ring of fire and you must fight two Stalfos to save her. She releases recovery hearts after this battle. There is a ReDead on the bridge in the central room, but you can't use your Ocarina so you'll just have to get frozen and run away. Go outside.
You and Zelda will be all happy, thinking Ganondorf is gone for good, but then you hear a suspicious sound in the ruins. You must go in and investigate. Surprise: it's Ganondorf! He turns into Ganon: an enormous pig-like beast, wielding two big swords. He will attack (you can't avoid this), knocking the Master Sword out of your hands and beyond the ring of fire where you can't reach it. Why can't Zelda toss it to you? I have no idea. That's just the way it is.
This battle can potentially be fairly easy, at least when compared to the fight with Ganondorf's human (Gerudo?) form. You WILL need a refill on magic, so hopefully you have some green or blue potion. If not, you can still win, but it is harder.
Equip Biggoron's Sword or the Megaton Hammer. Z-Target Ganon, get out your bow, and let him come close. For a moment, he'll sit there staring at you with those terrifying glowing eyes; this is your chance to shoot him point-blank in the face with a Light Arrow. Once you do that, stay locked onto him and roll right under him. Your Z-Targeting will automatically shift to his tail, which is his weak spot. Without the Master Sword, you must either use Biggoron's Sword if you have it, or the Megaton Hammer. As soon as you hit his tail, do a backflip so you don't get hurt when Ganon turns around. If you wait too long when Ganon pauses, he will slash at you, so do a backflip to avoid it.
If you are ever in need of magic, arrows, hearts, or anything else, wait behind some rubble and Ganon will break it apart, releasing recovery items.
If you use up all the rubble and have no potion and no magic left, you can try to roll under Ganon when he pauses and hit his tail extremely quickly before he can turn around.
Eventually Ganon will collapse for a moment and Zelda will call to you; the fire has gone away temporarily so you can get the Master Sword. You will need it, so grab it (if you don't, the battle will never end), and start using it on Ganon's tail instead of Biggoron's Sword or the Megaton Hammer. Eventually, Ganon will collapse again, and Zelda will use her power as a Sage to freeze him. Slash Ganon's face with the Master Sword (no other weapon will work) and you'll witness Ganon's bloody demise.
Congratulations! You beat the game! I won't spoil the lovely ending, but one little note: when the ending is complete, if you wait a while (a long while) you will hear Scarecrow's Song played six times with six different synthesized sounds, one minute apart. If you didn't record Scarecrow's Song, you don't hear this. But if you did, it's kind of cool. Enjoy!