Go west from Turtle Rock to Ganon's Tower. The seven maidens will use their power to break Ganon's seal so that you may enter the tower.
Descend to the 1st floor using the stairs on the left. Knock the key off the pillar and go left.
Knock down the moles using your hammer and then push the middle block. Underneath is a star tile which will allow you to get to the door on the left.
Use your Hook Shot to get to the south end of the next room. Hit the crystal to make it blue, set a bomb, and quickly pass over the blue blocks before they pop back up again.
In the next room, place a bomb next to the crystal on the left and hurry across the red blocks before they pop up. If you place the bomb too close to the crystals, they will both trigger and the the crystals will stay red.
In the room at the other end of the teleporter, push the block standing by itself near the west side of the area to make a treasure chest appear and use your Hook Shot to get over the chasm.
Step on the right teleporter, then on the one below you, then the one on the bottom-left corner of the room. After two more teleporters, you'll be out of those rooms.
In the next room, go to the northwest corner of the room and use the Firerod on the torch to the right. Hurry across the bridge that appears before the torch goes out and you can no longer see the bridge.
Place a bomb in the bottom-right corner of the room and fall into the hole to the basement.
Defeat the knights with your bow and silver arrows. It will be trickier to beat them than the first time because the floor is all ice, but with the Silver Arrows, they will die with one hit. Take the Big Key from the chest in the room to the north.
Ascend to the 1st floor and take the Red Mail from the chest.
Return to the 2nd floor and then climb up to the 3rd.
Push the block in the northwest corner of the 1st room to open the door.
In the 4th room, the button to open the door is underneath the middle skull below.
At the end of the 4th floor, you will have to fight the boss from the Desert Palace again. With the most powerful sword, however, two hits will kill each of the worms.
Cast Ether and the bridge in the 1st room will flash, or try to find it by trial and error. Defeat the three wizards and the door will open.
In the room with the four torches and the spinning flames, pick up all the skulls so that the torches aren't blocked, light all four torches with the Firerod, and quickly run to the exit before the door closes.
On the 6th floor, light all four torches in the 1st room to open the door.
In the third room, use a bomb and quickly throw it against the wall so that it is carried to the left and will blow up at the right time.
At the end of this floor, you will have to fight the boss from the Tower of Hera again. Try not to get knocked off the side.
Use your Hook Shot to get over to the chest that just appeared and go to the top floor.
Use the same technique to defeat Agahnim as in your previous battle. Deflect the beams so that they hit the real wizard and not the images.
Once you have defeated Agahnim, Ganon will leave the wizard's body, turn into a bat, and fly to the pyramid. Link will use the flute and follow him.