The Forsaken Fortress is located in the far Northwest quadrant of the Great Sea in The Wind Waker, and it's where Ganondorf has constructed his temporary lair. It's an evil-looking island, and most people tend to avoid it. The stone fortress is well-guarded with cannons, searchlights, and hordes of Miniblins and Moblins, who patrol and attack any would-be invaders. The Helmaroc King has made his home on the Forsaken Fortress as Ganondorf's servant. It is also the place where Link's sister, Aryll, is held prisoner, along with Mila and Maggie.
Breaching the Fortress Walls
After being launched into the fortress, turn right and you will learn that Tetra has slipped a Gossip Stone into your pocket that allows you to communicate with her over long distances. When she finishes talking to you, head up the sets of stairs and get caught in a searchlight. You'll be thrown into a jail cell.
Tetra will tell you to try to hide yourself. Whenever you're thrown into this cell, hop up onto the table and run towards the empty shelf. You will climb up on top of it. When you do, throw the pot away and crawl in through the hole in the wall until you get out.
The first time you get out, head down the path and get the contents of treasure chest in plain view -- the Dungeon Map. Hop at the torch and swing across it like you did in with Niko. Enter the door on the left.
Paving Through the Fortress
Outside, turn left and climb the ladder. Fight the Bokoblin here. You must beat him by hitting him with a stick. There is a pot of sticks nearby that you can take from, or you can make him hit your shield and the stick will fly away from his hand. Either way, defeat him. Hop back down the ladder and go back into the room you came. Enter the other door now, going counter-clockwise around.
Turn left, go up the ramp and defeat the Bokoblin the same way. Go back down the ramp and continue along the counter-clockwise path.
In this room, get the compass, swing across the torch rope to the other side, and go through the door. Turn left again and go up the ramp and up the ladder, and defeat the Bokoblin the same way. Go back down and continue counter-clockwise. Again.
Hop over the gap the same way. If you want around 40-50 rupees, push the block to your left down, grab the rupees below, and push the block under the ladder to get back up. Continue going counter-clockwise again.
This is probably the hardest part of the dungeon if you don't have patience. Find the barrel to your left and pick it up. You will put it over your head. Now head the only way you can that isn't off a ledge. When you get close to a Moblin, it might see you if you're moving, so stay still in the barrel. If you get caught, you'll be thrown in the cell, so just find your way back here again. Head towards the big door and open it (not while you're still in the barrel).
Head up the stairs and do the same thing with this next barrel, avoiding the Moblin. When you are out of his sight, continue up the path. You'll encounter a gap in the floor, but just sidle the wall to cross it. Do this for the next gap too. Continue up the path for a short mini-boss-esque fight.
Grab your sword off the ground and use it to beat this guy. Be mindful that he has a shield, but you can beat him pretty easily without paragraphs of strategy. When you do, the door will open, and you can enter. This will begin the next cutscene.
Words of Warning
If you don't take down all the Bokoblins in all the search lights, once you get caught you'll be thrown in jail and you have to start all over. Also, since you don't have the sword, your barrel is where you hide in. You'll hear a sudden music if Moblin see your barrel move. It's not normal if a Moblin see a barrel move and if it did, same thing would happen!