Now that you have all of the eight pieces, the Triforce of Courage will be reconstituted. Before going on with your quest, refill your arrows and bombs. You can also look for small fairies from the springs and/or buy some potions from the Windfall Island chemist. You can also go looking for Pieces of Heart. When you feel ready, play the Ballad of Gales and head for the Tower of the Gods.
Sail to the surrounding wall and go to the entrance. The King of Hyrule will see the Triforce complete again and its symbol will appear on your hand. You will then end up in Hyrule Castle.
Get inside the castle and down to the underground. Zelda has been captured by Ganondorf. Get rid of the two Darknuts with the Hurricane Spin, then go back up. Head towards the other entrance and get on the bridge. When you see the light shield, raise the Master Sword to break down the barrier. Go forward, follow the path, then use the Hookshot to cross the gaps. Get into the cave and open the door.
Go ahead to the centre and follow the first bridge on the left (however you still can follow them in any order).
Open the door, shoot the Hookshot at the bar and jump on the small platform. Do the same to reach the second one, then use the Hookshot on the third bar and climb up the rope. Use the Deku Leaf to fly towards the door and open it. You will find Gohma (the same one from before?), and you will only have at your disposal the weapons you had during the first fight against it. Attack it the same way you did before and you will return to the centre of the big room.
Open the next door on the left (clockwise). Use the Deku Leaf to make the leafy pinwheel move and jump on the platform. Use the Deku Leaf again (to the maximum) to go to the other side. Jump on the big branch, then switch on the second pinwheel. Use the Deku Leaf again and fly towards the second platform. Switch the pinwheel on again, then fly towards the right branch, then the left one. Thanks to the Deku Leaf, fly towards the door. Shatter the nuts to refill hearts and open the door. Time to meet Kalle Demos again. Use the same tactic to beat it and you will return to the middle room.
Follow the bridge and open the next door. First, run through the corridor to avoid the coffins and climb the stairs. Go through another corridor, then backtrack, aim the light at one of the Chuchus, carry it and drop it on the switch. Walk through the corridor again and swiftly go through the stairs. Once more, run through the corridor, draw at you at least one Chuchu to turn it into stone, then carry it and backtrack, place it on the switch and run swiftly towards the stairs. Open the door and fight Jalhalla again.
Back in the big room, open the last door. Get rid of the Wizzrobes with some arrows, then get on the spring, put on your Iron Boots and get propelled to the other side. Walk between the two tornadoes and land next to the vases. Fight off the enemies, shatter the vases to refill your hearts, then shoot the Hookshot at the target on the wall and open the door. Fight Molgera like you did the first time (be even more careful about the sand's colour). In the big room, the door with the four symbols will shatter, and you can reach the second part of the dungeon.
Get rid of the small devils, climb the stairs and open the door. Open the door on the right. Take a good look, listen to the King of Hyrule's message, then get near the torch and read the writing on the stele. Jump into the hole. Phantom Ganon is here waiting for you. If he casts energy balls at you, reflect them with your sword and hit him when he falls. If he casts pink balls at you, use a Spin Attack to reflect them, and if he summons some clones, avoid them and wait for them to disappear to attack them. Finally, according to the clue on the stele, open the door shown by the hilt of the sword. Repeat those steps a couple of times until defeating Phantom Ganon in a different-looking room. Pick up the Light Arrow from the chest and open the door to get to the previous level. There, you will be attacked immediately by another Phantom Ganon. Shoot a Light Arrow at him to defeat him once and for all (if the clones appear, avoid and attack them). Then open the left door. Be careful of the order in which the torches are shown to you, then use the Boomerang in the same order (from left to right: third, first, fourth and second). The King of Red Lions will appear and tell you that you can get back on the surface by getting into the light aura. Unless you are running short of ammo, leave. Pick up Phantom Ganon's weapon and throw it at the next door.
Follow the long alleyway while getting rid of the enemies and shatter the pots to get some ammunition. Open the door leading to Ganon. You will finally face Ganondorf with Princess Zelda sleeping. The Lord of Evil is ready to fight you!