Ganon's Tower
Get in the centre of the tower. Climb the stairs, open the door and fight the two Dinolfos. Open the next door, climb the stairs, get rid of the Stalfos and take the Boss Key in the chest. Go on, attack the two Iron Knights by waking them one at a time, and again climb the stairs. Open the boss door. In the room with a huge pillar in the middle, avoid breaking those pots now and open the door on the right. Climb the remaining stairs to find the lovely Zelda and the dear...
Ganondorf
Here, you find the Evil Lord playing the organ, while the Princess of Hyrule is still locked inside a crystal cage. Then the pieces of the Triforce awaken and get together. Navi is forced to step away and to let you fight Ganondorf on your own...
First, immediately go near a wall, because the centre of the room will go down. As with Phantom Ganon, the goal is to reflect his attacks with the tip of your sword. Stand in front of him and reflect his energy balls until he gets hurt. At this moment, immediately shoot a Light Arrow at him, if he gets hit, he will fall. Quickly run to him and strike him with your sword several times, then go back to a wall and do it again. Sometimes, he uses another attack, some sort of rain of lightning. As soon as you see him preparing this attack, load your sword for a Spin Attack and release it when lighting is about to hit you. He will get hit as well and you can shoot a Light Arrow at him. If you fall down during the fight, you can break a few pots to refill your hearts, magic and arrows, then go back up using your Longshot on the main pillar.
Once Ganandorf is defeated, Zelda is freed. Follow her to the bottom of the tower, stay right behind her or wait for her at the next gate. On your way, she will be caught in a flame wall, quickly get rid of the two Stalfos to set her free. You will also meet a ReDead, avoid it or attack it on the spot. Then the tower will crumble for good.
Once you got away from the dark tower, you hear a noise. Step in the middle of the plaza to fight Ganon!?!
Ganon
Under his true form, Ganon will take your Master Sword away, but you still have your Biggoron Sword. Equip it (or if you don't have it, use your Megaton Hammer). To begin with, use the Z lock to slash his tail several times, then when Zelda tells you to, take back your Master Sword so the second phase of the fight can start. Go back to the middle of the plaza, then step back, use the Z lock to aim at his head and shoot a Light Arrow to stun him. Then, run behind him and strike his tail again. Step back and repeat these actions until he stays down. When Zelda asks you to, deal him the final blow!
Zelda and the other Sages can now open the sealed door and send Ganon back into the void of the Evil Realm. The latter vows to get revenge, and unfortunately keeps the Triforce of Power. Link then gives back the Ocarina of Time to the Princess who brings him back to his own time.