The Legend of Zelda: Ocarina of Time Master Quest/Ganon's Castle
 Main area
Just as you go forward, you'll see two Green Bubbles patrolling the staircase. Dispose of them with your bow and continue. You need to kill all the enemies to open the door leading into the main room. The two Armos Statues should be no problem since they can't actually engage you from the pillars they're standing on. The Iron Knuckle is the real problem here, because of the floor spike, the lack of health refills in this room as well as the awkward room layout. You may want to resort to bombs to kill him at a distance. Once all enemies are gone, the door will unlock and you can go through.
You're now in the main area. There are six barriers here which prevent access to the central tower where Ganondorf dwells. You will need to complete six trials to dispel the barrier, each of the trials being based on a particular temple you have visited before. Even though it may not seem like it, these trials have to be beaten in a specific order. If you need to heal, there's a secret passage right below the entrance - drop down and look for a secret passage using your Lens of Truth, it leads to a room with lots of fairies and Business Scrubs. Once you're ready, start off by entering the Forest trial directly to your right.
 Forest trial
The first room starts off with a rather straightforward fight against two Stalfos. Once they're gone, look above the door - there's a small key and a fan there. Use the Longshot to pull yourself up to the torch, then run across when the wind isn't blowing (or just use the Iron Boots) to get the Small Key. Continue by going through the door.
The next room is a real challenge. There are lots of fans and Beamos statues scattered all across the room that are just there to make life hard for you. There are two eye switches here, but shooting them is of no use (you get bombs and arrows if you were to do this). Look to your right to notice a fan. Equip the Hover Boots, and once the fan starts blowing, run into the air stream to be blown to the platform on the right with a Beamos on it. Quickly kill it with bombs before it can hit you (or stun it by shooting its eye), and run across the platforms until you're at the locked door on the other side, destroying all the Beamos on your way.
Once you're at the locked door, wait until the fan to the right of the locked door (with a Beamos right in front of it) is not blowing, then get on the platform and equip the Iron Boots so the wind won't blow you away. Play the Song of Time to move the nearby block down and reveal an Armos Statue. Play the Song of Time once more and the block will move back up, but the statue will drop down onto the switch which opens the door. Now, jump back across and go through the door. Shoot the Forest Barrier with a Light Arrow to dispel it.
You'll be returned to the main area. Go to the right and enter the Water trial.
 Water trial
Once you enter the room, you'll find that it is full of Freezzards. You may want to use Din's Fire to get rid of all of them easily. In the center there's a Blue Fire flame, but it is covered by a water jet. There are two ways to get to the Blue Fire: for the first, go to the right and you'll notice a single of Dead Hand's hands just standing there. Kill it with your sword and strike the pillar behind it which will make the water jet go out for a short period of time. The second, and easier, way is to simply equip the Hover Boots, roll into the water jet and pull out your bottle, which will make Link catch the flame just as well.
The chest to the left inside the red ice just contains 20 Rupees. Instead, go forward to the door and release the Blue Fire to melt the red ice blocking it. Catch some more Blue Fire and go through the door using the leftover Small Key from the Forest trial to enter a block puzzle.
In here, you'll have to collect five Silver Rupees. First of all, pull out your bow and get rid of all the Keese flying around (beside those you see, there's also an invisible one here). Jump down and fall into the hole in the middle to get your first Silver Rupee. Go to the back and jump across the pit (the Hover Boots make this easier) for the second one. In an alcove beside the blocks you'll find the third one, and by jumping from one of the blocks to the other you can get the fourth one as well.
For the fifth one, grab the block furthest away from the wall and push it to the small rock ahead, then push it to the right so it falls into the pit where one of the Silver Rupees was. Afterwards, go to the other block, push it forward across the now closed pit, then left twice so it moves into the alcove. Climb the block and up you'll find the Silver Rupee inside a block of red ice. You do not actually need to melt the ice - simply jump attack the red ice block and you'll get the Silver Rupee, opening the door.
The door, however, is unreachable. Exit and re-enter the room to reset the blocks' positions. Push the block straight ahead to the now unlocked door and use your Blue Fire to melt the red ice barrier. Go through the door, and shoot a Light Arrow at the Water barrier to dispel it.
Once back in the main area, go to the right and into the Shadow trial.
Note: If your jars are empty, go out and refill it with fairies to help continue with your survival.
 Shadow trial
This is another Silver Rupee puzzle. First of all, you should kill the Green Bubble flying around right in front of you. From here, it may seem like there is no way to continue, but shoot the bomb flower you see at the right to make a treasure chest appear on the other side. Use your Longshot to latch yourself to it, then open it if you want (it contains arrows).
Here, look forward and take out the Lens of Truth and you'll discover an invisible platform that moves diagonally across the pit. Equip the Hover Boots and walk over to it as it moves towards you (it's kind of tricky). From here you can collect the first Silver Rupee, and by walking over to the bomb flower you shot earlier, you can get the second Silver Rupee as well. Walk over to the platform with the Beamos and kill it, as it hides the third Silver Rupee.
Here, you may notice a torch submerged into the ground. Use a Fire Arrow to light it and a platform will appear so you can get across the next pit. Get on the platform, pull out your bow and turn around to discover an eye switch, which will make a treasure chest appear. Walk over and open it to get a Small Key. Use the Lens of Truth again and you'll notice an invisible path branching off to the left. Follow it to a lone platform with a Beamos, kill it to acquire the fourth Silver Rupee.
Return to the previous platform. With the Lens of Truth you can see another invisible path leading to the exit. However, there's a gap with a guillotine on the way, and if you are not careful it will hit you and knock you down the pit, forcing you to start over. While crossing the gap you'll collect the last Silver Rupee on your way, which opens the door at the end. Go through and shoot a Light Arrow at the Shadow barrier to dispel it.
Once back in the main room, go to the right. You can't do the Fire Trial right now, so continue walking around until you come across the Spirit trial. Enter it.
 Spirit trial
As soon as you enter, kill the two Fire Keese and the Torch Slug. Turn around and you'll see a depressed eye switch above the door you just came through. Shoot it and an Iron Knuckle will appear in the room. You'll have to fight him, but make sure he destroys the pillars in the center of the room, as they hide a rusted switch that is the only way to continue. Kill the Iron Knuckle, and use the Megaton Hammer on the rusted switch to open the door to the next area.
In here, immediately kill the Green Bubble right in front of you. Open the chest you see to get some Bombchus. Look at the bars and you'll see an opening at the ceiling. Stand right below the opening, turn your back to it and drop a Bombchu - if you positioned it correctly, it should run up the wall, go through the opening and hit the crystal switch on the other side, which opens the door. Go through and kill the Green Bubble you find here as well.
The path ahead has a Gibdo and two Redeads. Play the Sun's Song to stun then, then walk through to the room with all the sun faces and use Din's Fire to kill all the threats. Look above you to notice a spider web, shoot a Fire Arrow at it and it will burn down, allowing light to pass into the room.
First of all, shine light onto the sun face to the right of the locked door. A treasure chest will appear, open it to get the Golden Gauntlets! Now, turn around exactly 180 degrees and you'll be facing a sun face that, when lighted, makes a treasure chest with a Small Key appear. To continue, stand in front of the locked door and reflect light onto the Spirit symbol above it. A sun face hides behind, which opens the door when activated. Go through and shoot a Light Arrow at the Spirit barrier to dispel it and return to the main room.
With the Golden Gauntlets, you can now go and get the double health upgrade from the Great Fairy just outside of Ganon's Castle. Once you're ready, walk around the main room to notice a large black block. With the new Golden Gauntlets, you can lift it to reveal the door to the Light trial, which is your next destination.
 Light trial
In the first room, you're pitted against two Torch Slugs and a Dinofol. The Torch Slugs are very annoying in their habit to ambush you so you might want to take them out first before bothering with the Dinofol. Once all enemies are dead, the door to the next area will open. Here, there's a Triforce symbol where you can play Zelda's Lullaby but it's worthless (you get a Recovery Heart if you try), so instead go ahead and open the locked door.
Here, you're in a room with a rolling boulder and a Beamos in the center. If you try to walk around you'll see that flame walls prevent your progress. While the Beamos is not facing you, throw a bomb at it to kill it, which will allow you to see a Hookshot target at the ceiling. Use it to safely get across the room, and open the locked door at the end to get through.
This room may now seem like a trap, because there is no barrier to disspell. What to do? Go to the right torch and hit it with your sword. As it turns out, a crystal switch is hidden inside. With it enabled, try to go through the wall and you'll just pass through. On the other side, you'll finally find your Light barrier, which you can shoot with a Light Arrow to disspell it.
Once back in the main room, go to the left to enter the Fire trial.
 Fire trial
As soon as you enter, equip the Goron Tunic and the Hover Boots. This is a very difficult Silver Rupees puzzle and it will probably take you lots of retries. You'll have to restart if you fall into the lava at any point.
Jump to the platform moving back and forth. At the right you'll see a pattern of four platforms. Get to the right one at the back and it will launch you upward. Backflip from here to get the first Silver Rupee, and be sure to not fall off the platform and into the lava while you do this!
Now, look to the left and you'll see a platform with two Torch Slugs and a black block. Walk across it and throw the black block away - it will serve as a stepping stone later on. You should notice a Silver Rupee over the lava - wait until the moving platform gets over there then jump on it to grab that rupee. Look ahead to see a Hookshot platform, use your Longshot to get to it (immediately climb up so you don't slip off into the lava right away!), then jump off to the left to grab another Silver Rupee.
From here, jump across to the next platform, and then to the right. It will launch you upward, and from here you'll have to get across to the black block you threw earlier to get the Silver Rupee on top of it. This jump is very tricky and hard to do, and it might be easier to try it as your platform moves down (or up) so you can control Link better.
Now, cross the platforms until you get to the one with the Beamos and the other black block. You'll need to time it so the moving platform comes to you as you're coming across, otherwise you'll just fall into the lava. Once there, immediately stun the Beamos and kill it with bombs. Throw the black block away and you'll see it was hiding the last Silver Rupee. Collect it to complete the puzzle.
A Hookshot platform will now appear beside the exit door. Walk back across the platforms and target it with your Longshot to get across. Go through the door and shoot a Light Arrow at the Fire barrier to dispel it.
With all the barriers disspelled, you can enter the central tower now. Cross the bridge and get inside.
 Inside Ganon's Castle
The inside of the tower is exactly identical to the one in plain Ocarina of Time, so refer to the OoT guide for details.
The Ganondorf and Ganon fights, including the escape sequence, are perfectly identical too.