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This part will take you through the second floor of Ganon's Tower.
The Point Of Return
The room you enter in has two doorways you can enter through, and one door that you can't just yet. Go to the door on your right and watch the candles on the wall, in the order that the game will show you. Then go back into the main room and go to the door on the left. This room will show you four crystal switches in the same order as the candles in the other room. Get out your Boomerang and target all four switches in the order shown. A black portal will appear in the water before you, and briefly spooking Link as he approaches is the King of Red Lions. He will tell the boy that this portal was used by Ganondorf which connects between his tower and the Forsaken Fortress. If we want to, we can use the portal and return to the world above at any time prior to facing off against Ganondorf. This would be a good way to replenish lost supplies before we get to the final battle itself.
The Phantom Puzzle
Head back into the room with the candles and drop down the hole to begin a torturous maze of identical rooms with four doors. In each of the rooms, you'll face off against multiple Phantom Ganons and find which one among them is the real phantom. Slash at the real one with your sword, and it will drop its sword. The direction that its handle is pointing to will be the door that you must go through, indicated by the "secret found" sound commonly heard in Zelda games. Of course, you can simply avoid fighting the Phantom Ganons in the succeeding rooms and just follow the pattern of straight (from where the handle of the first sword points to), left, straight, left, right, and straight. In the final room that you enter, you're going to have to play energy bolt tennis with Phantom Ganon again, swatting it back and forth until it hits either you or him. Strike him with the sword when he's stunned, and he will vanish, leaving his sword behind. A treasure chest will appear, which will give us our last useful item -- the Light Arrow. These things do instant damage to even tough enemies that are not bosses. However, we want to save as many as we can for dealing with Ganondorf.
Up the staircase
The metal bars on the door we went through to get in here will be raised. Go through that door and we'll return back to the room with the one door that we can't open. Phantom Ganon will return with his copies to harass you once more. Get rid of his copies and use a Light Arrow to instantly put him down. He will leave behind his sword that we can use on the door that we can't open, allowing us to go up a series of staircases to the final boss fights. Along the way we'll have Moblins and Darknuts to deal with, but they just don't stand a chance against the Light Arrow. Before the big bolted door there are two Mighty Darknuts that we need to defeat in order to lift the bolt from the door. Once they're out of the way, use a bomb to blow open a teleportation pot in this room, then go through the door and get ready to rumble!