Pirate Ship and Forsaken Fortress

Other than breaking barrels and vases, there's only one thing to do on the pirate ship: beat Niko's challenge. Head down into the hold and find Niko. He'll explain what to do. Step on the switch, and then jump forward to the swinging lamp. Note that you can stop swinging and adjust your position by pressing and holding the R button. Jump from lamp to platform and platform to lamp until you reach the other side. Niko says there's a time limit, but it shouldn't be an issue. When you make it across, Niko will let you open the treasure chest, which contains the spoil's bag. Finish bashing all the barrels and vases for rupees, then head up to the deck and climb into the crow's nest to speak with Tetra.

After your unheroic journey to the Forsaken Fortress, you'll find yourself sans sword. Not to worry--grab one of the barrels near the first set of stairs and you'll have yourself a makeshift disguise. Climb the steps and proceed cautiously past the searchlights. You have a moment to stop once a searchlight (or a guard) sees you, but don't move again until you're in the clear. Gather up the rupees and then go through the huge wooden door.

Getting caught in the spotlights will land you in jail.

Rats. This is your first encounter with these varmints, who will bump you and steal your rupees. Note that you can place all-purpose bait in front of a rat hole, and they will offer to trade you something. You can explore the ground floor of the fortress and find some loot. But eventually you'll want to get to the second floor, and the easiest way to do that is to get caught. Let one of the spear-wielding guards see you, and you'll get tossed in the slammer.

Climb onto the table and jump to the bookshelf. Smash the vase and crawl into the hole it reveals. Follow it around until you emerge a free man. Follow the hallway to a ledge with a chest, which contains the dungeon map. At this point, you'll want to drop back down to the first floor and search the nearby barrels for a switch--step on it and a chest will appear, containing a "piece of heart." Don't worry if you miss it the first time, you'll be back to the fortress later. After you get the piece of heart, get caught and escape again.

Smash this vase to get out of the jail cell.

Return to the ledge and jump to the lamp. Swing across to the opposite ledge and go out the door on your left. Hang another left and climb the ladder. Continue up until you reach a bokoblin manning a searchlight. There's a vase nearby with some sticks in it. Smash the vase and grab a stick, which you can use as a weapon. When the guard is eliminated, the searchlight will stop operating. Head back down and then back into the room where you got the dungeon map.

Take the other door, and once again make a left. Continue up until you find another searchlight. Once again, smash the jar and grab a stick to use as a weapon. Defeat the guard to disable the second light.

Looking at the dungeon map, note that there are two routes through the second floor. The route that goes along the eastern side is the better of the two, if only because it makes sneaking past the final guards a bit easier. So head down and then continue to the right. Grab the compass from a chest, and then swing across the gap. Go through the door, make a left, and head up to take out the last searchlight.

Find the compass behind these barrels.

Once the last searchlight is disabled, climb back down and continue along the eastern path, swinging over ledges when needed. Before you enter the northernmost room of the floor, make sure you push the box into the courtyard--it will make returning to this point easier should you get stomped, because it grants access to that ladder you may have seen when you first entered the fortress.

In the northernmost room, don a barrel and sneak past the guards to the stairs. Go through the wooden doors. Outside, you'll need to grab a barrel and sneak past another guard. This can be sort of tough, so be patient. Just stay absolutely still until you are sure he isn't looking, then scoot past him. You'll come to a narrow ledge--walk to the wall until the action on your A button reads "sidle." Press the button, and work your way across. You'll need to do this once more, and then you'll find your sword. Fight the guard, then head through the doors to find Aryll and start a cutscene.