Go back to Castle Town, to the main plaza, then north towards the castle. Using the Fused Shadow's power, Midna will turn into a kind of spider and destroy the dark magic shield covering the castle. Go ahead and push the two next doors.
Go towards the east. When magical walls appear, attack the Bokoblins and open the door on the right.
Go to the centre, then a fight against lots of Bokoblins will start. Once the barrier is down, go right, then head north and pull the lever close to the fence. Go ahead and fight a much stronger enemy. Let him get close and hit him when his weapon is stuck in the ground or use your Back Slice to hit his back. Repeat these steps a few times, then get away when he starts to spin. As soon as the "spinning sound" stops, run to him and strike him. Do this once again and he will go away leaving a Small Key behind. Pick up 20 rupees in the chest next to the torch and climb the southern stairs (to stand in the middle of this garden). Jump to the southwest, pick up 20 rupees in the chest, then go back through the south door.
Now head west. When magical walls appear, attack the Bokoblins, then open the door to the left.
Watch out for the enemies' arrows, go towards left and go around the central wall to the east. Ride one of the boars, then come back to the west and speed up to break the planks, along with those to the north. Go to the back of the garden and throw the Gale Boomerang at the leaves on the ground to discover a Triforce symbol with a green line. Stand with your back against the fence and look at this line and the six columns with a propeller atop of them. Aim and lock these propellers to copy the green line's path: the closest column to the Triforce, then the right one in the middle row, then the left one on the middle row, then the one in the middle of the back row. The fence being open, go north and pick up the Map in the chest. Then turn into a wolf, come back to the Triforce and dig where your senses detect something, to the north of the map. You will get out in a new location.
Go north and get rid of the Stalfos along your way. (A bomb is needed to get rid of the bigger Stalfos.) Look at the writing on the two tombstones to the west, then turn into a wolf, use your senses and look at the soldiers next to the tree to the north. Turn back into your human form and drop a bomb on the small heap in front of the tree they are all indicating. Step on the switch which will raise a gate, go west and open all three chests to earn 121 rupees. Dip your Lantern or an empty bottle in the oil jar, then light the torch close to you, which will make the rain stop for a few seconds. So run to the east and light both torches next to the fence to raise it. Now you can use your Dominion Rod on one of the two owl statues to bring it to one of the recesses to the south (close from where you come from). Bring the other statue to the other recess, then climb on the blocks to the southeast. Jump on both statues, then go west. Pull the handle to raise the gate and open the chest to get another Small Key. Come back to the statues, turn into a wolf and dig close to the south wall to come back to the western garden. Climb the ladder next to the chest that contained the Map, go on to the south and pick up 10 rupees/Sad Zelda stamp in the chest. Jump towards the entrance of the garden and open the door to go back to the central garden.
Climb the stairs leading to the castle and unlock the door.
Inside the castle
Get in the hall, then fight Bokoblins and Lizalfos within the magical walls, which makes a chest appear. Climb the stairs to the west, shoot your Clawshot at the chandelier, let go and open the chest containing the Compass. Then latch on to the chandelier to the east, go down using your Clawshot's chain, then hook onto the next chandelier, let go and open the door north.
A Darknut is there! Same as usual, use all the hidden moves you learned during your quest to shatter its armour, then get rid of its shield and defeat it. As long as it has its armour and heavy weapon, you can get close to it and quickly step back to force it to attack you, then make good use of the few seconds it's stuck to get close and hit its side or back. You can also get close and use the Shield Attack and Helm Splitter. When it only has its sword left, you can use your Back Slice to hit its sides or back. Once it's defeated, refill your Lantern in the eastern jar, then light the two torches to the west so two steps appear. Climb on them, then turn towards the torch close to the oil jar. Throw the Gale Boomerang at the torch to put it out, and as soon as the torch is put out (don't wait for the Boomerang to come back to you), go back to climb the last step. If you miss the last step, light again the torch, then climb back both steps and try again. Pick up the 50 rupees in the chest.
You have now two corridors leading to the third floor and the choice is yours. The western corridor is the easiest, the eastern corridor is way harder, but rewards you with 250 rupees, but nothing prevents you from clearing both!
Western corridor: Do go west and open the door. Light the torch in the middle of the corridor to have some light, then quickly find the painting on the east wall and shoot an arrow at the rope to make it fall. Look at the drawing on the wall, then quickly light the torches in this order: the one right of the drawing, then the one diagonally across, then the one left of the drawing and the one diagonally across the third one. The bars on the next door will rise. Open the door to the south.
Fight off the two big Lizalfos, starting with a spin attack, then open the door to the east. Step on the switch to lower the chandelier, then come back to the corridor and open the west door to go outside.
Eastern corridor: Do go east and open the door. Get rid of both Lizalfos, starting with a spin attack, then look closely at the paintings on the walls. Shoot an arrow at the rope of the different-looking painting (the pink one), then shoot an arrow at the blue diamond behind it. Open the next door.
Here come two more Darknuts that you have to fight following the same strategy as before. Get close to one from its side so the other one stays still. After defeating them, open the door to the west. Pick up 50 rupees in the chest to the left, then step on the switch to make a chest appear to the northeast. Jump down to the first floor, come back to the door leading to the first Darknut, then shoot your Clawshot at the chandelier to the east, let go and open the chest to get 200 rupees! Go back where the two Darknuts were. Open the door to the east leading outside.
Outside the castle, if you're coming from the eastern corridor, go straight ahead and some enemies will appear! With your friends' help, go ahead to the south and pick up the Big Key in the chest. Then go to the other side towards west and fight the Aeralfos like you did in the City in the Sky. Go ahead to the south and pick up the Small Key.
If you are coming from the western corridor, you can start by fighting off the Aeralfos to the west, then the other enemies to the east to eventually get the two keys. Come back to the middle of this open area and unlock the door.
Turn into a wolf, use your senses and get rid of the phantom rats by doing a spin attack. Get close to the ghost and watch it stretching its arm. Jump in this direction while staying close to it, then get close to the next ghost and jump where he shows you to, and so on. So go through the room like this: from the start: north, west, south, west, north, west, then turn back into your human form. Climb the damaged stairs to the north, fight two Lizalfos, then get close to the next stairs. Shoot your Double Clawshots at the torches to go across the corridor and let go at the end of it. Fight some more Lizalfos and keep on going up. Now use your Spinner on the tracks while avoiding the traps. Start from the east side, jump to the left, then to the right and if needed once more to the left to reach the next room. You must now fight off another Darknut to gain access to the two doors.
Once the Darknut is down, unlock the door to the left and open all the chests to refill your arrows, bombs and loot about 400 rupees as well as the Happy Zelda stamp on Wii U. Also put a fairy in an empty bottle (no need to stock any oil from now on). Then get out and open the boss' door.