With the Master Sword in hand, Link heads back to the Forsaken Fortress to face Ganondorf
Enter the Forsaken Fortress
As you get close to the Forsaken Fortress, try to avoid getting hit by the cannons and things, then sail up to the wooden door in the south wall of the fortress. As soon as you're close enough, get your cannon ready, and quickly hit the top of the door to bomb it to pieces. If you're lucky, you won't get hit by the cannons. Cruise through.
Your boat will talk to you. Now that you have the Master Sword, there is no need to sneak around like before. Go up the stairs to the searchlight area, and go toward the big wooden door, where a fight starts.
Phantom Ganon
Nintendo Gallery Note: You can fight this enemy later, but at that point you will want all of your picto slots free for other things. Make sure Phantom Ganon is floating above you but far away, and make sure that he is not about to throw an orb at you. He can have an orb in his hand when you take the pictograph, but make sure that he hasn't been holding it for very long, because otherwise he is about to throw it.
Swing your sword to hit the orbs of energy back at Phantom Ganon. Sometimes he vanishes and reappears at different places. If he reappears close to you, usually behind you, that means that he is about to hit you with his sword. You can either roll away, or quickly turn, lock on, and hit him with your sword. You'll be able to hit him a few times before he disappears again. When he is floating far away from you, that means that he is about to throw an energy orb. You have to swing your sword at the right time: the orb has to be close enough for you to hit it with your sword, but not so close that it ends up hitting you instead. Keep hitting the orb back and forth until he falls to the ground. Let go of the L button so that you can run more quickly, and run up to him and hit him with your sword repeatedly. Keep using this strategy until he is defeated.
Receive the Skull Hammer
Open the chest to get the Skull Hammer, then fight off the miniblins and go through the big wooden doors.
Disable a Searchlight
In here, use the boomerang to defeat the rats that carry bombs. If they throw a bomb at you, run away. Turn right and go through the door that you see.
At the end of the hall, use the Skull Hammer on the posts, fight off more Miniblins, and go through the door on the right.
Try jumping out of the way if the moblins throw their lanterns at you. They don't throw the lanterns very far, so you should be able to just jump backward to get out of the way. Note that there are also rats with bombs in here. Defeat them with the Boomerang. Defeat the Moblins, collect the spoils, then go to the end of the hall where there is a cell. Defeat these rats with the Boomerang. The switch that opens the cell door is behind the barrels. Step on it, and open the chest inside the cell to get a Piece of Heart.
Make your way back to the first room, fighting monsters on the way.
In the first room, use the Skull Hammer on the posts, defeat the Moblins, and go through the door.
There is a black hole in the floor. It is a Floormaster. Much like Wallmasters from previous Zelda games, it tries to grab you and warp you to the beginning of the dungeon. In this case, you will get sent to the jail cell if it catches you. To defeat it, get close to it so the purple hand comes out, use the Boomerang on the hand to keep it from grabbing you, then attack it with your sword, then hit it with the Boomerang again and repeat.
Defeat the Moblin in here and go through the door.
If you stray from the wall of this room, you will get hit, so stay close to the wall and make your way to the bed with the chest on it, which contains 10 rupees. Climb up the ladders to the only platform that you can reach. It is the one with a ladder going up it. Go through the door.
You can disable some searchlights on your way through these halls, but it's not necessary because these two searchlights are only pointing at the courtyard. There is another searchlight later that you will have to disable.
Head straight across the hall and through the door. From there, go through the door to the left. After that, go straight across this hall through the door.
Defeat the Bokoblin, then jump and glide over to the other ledge. If you fall, just climb up the ladders to reach the ledge. Use the Skull Hammer on the posts, and exit the room.
Go through the left arch, go up the ramp, go up the ladder, and defeat the Bokoblin to disable the light. Then go back to the hallway that you came from, turn left and go through the door.
Jump and glide to the other side. Exit the room.
Go quickly through the door straight ahead to avoid getting hit by the Moblin statue above the door.
Defeat any Moblins that get in your way, and go up the stairs and through the big wooden door.
Find the Bird
Head up the stairs, keeping the Miniblins out of your way. More will show up no matter how many you defeat. Use the Skull Hammer on the posts, sidle across the ledges, follow the path to a post, and use the Skull Hammer on it to unlock the door. Go in and watch the cutscene.
When you're back in control, start running and rolling up those ramps around the room. The bird will knock out the ramps as you go up, and will also try to hit you, so roll to go more quickly. If you lose a ramp before you reach the other side, just wait to swim across. You need to hurry, so don't worry about the Bokoblins. Just hit them with your Boomerang to get them out of your way.
When the bird gets in your way, hit its face with the Skull Hammer. Climb up to the roof.
Helmaroc King
Nintendo Gallery Note: This is your only chance to get a picture of Helmaroc King. The bird needs to be pretty close to you to get an acceptable picture for the sculptor. Wait for it to fly away such that you can't lock on. Then wait for the bird to face you and come close to you. If the bird is over the tower, it is close enough. You don't have to get the entire bird in the picture, as long as most of the bird is there. Once you have taken the picture, be ready to roll away if the bird is flying in at an angle.
There are spikes on the walls, and occasionally the bird will try to blow you into them, so be ready to roll toward the center at all times. Note that you can't roll if you're holding L, so let go of it if you need to roll.
When the bird is flying, watch it closely. If it's hovering in one spot above the tower, start rolling toward the center to keep from getting blown into the spikes.
If the bird has flown away and you can't lock on it for a while, watch it by pressing up on the C-stick. If it comes towards you at an angle, roll out of the way because it will try to scratch you with its claws. If it's coming straight for you, wait for it to land. Then get close, let it walk a few steps, then go to one side of it because it's about to peck. It will get its beak stuck in the stone, giving you time to hit it with the hammer.
After that, avoid its attacks and let it get its head stuck again, hitting it with hammer each time until the mask comes off. At that point, it's vulnerable to the Master Sword, so start hitting it with the sword when its beak is still stuck.
When the bird is finally gone, go up the ramp and into the room on the piece of the ship. Watch the scene.
Mysterious underwater place again
Nintendo Gallery Note: This is your only chance to get a picture of Tetra. Take a picture of Tetra as she follows you. Try making her walk behind one of the flagstones in the water to get her stuck behind it. Get up on the stairs, move slightly to the side so she moves and gets unstuck from behind the flagstone, and quickly take a picture as she's walking toward you. Get as much of her as you can fit into the frame. As long as you have some of her head, all of her torso, and some of her legs in the picture, you should be okay. Getting Tetra's picture gets you figurines of all the other pirates for free.
Go inside with Tetra. Head down those stairs to the Master Sword chamber. Watch the scene.
Once the exciting events have unfolded below, go back to your boat, who will talk to you. Cruise into the glowing spot.