Time to do battle with Ganon. This is without a doubt the funnest battle of the game, as it's the one you've been building up to throughout the entire game, and it's not particularily easy.
After you walk up to the pile of rubble and are surrounded by a wall of flames Ganondorf will return and transform into his true form, Ganon.
You lose your Master Sword in this battle, but if you did the quest to obtain the Biggoron's Sword you can use that. I don't recommend it yet, trust me, arrows are your friend. All you have to do to hurt him currently is nail his tail. You don't need to hit his tail and then hit him with your sword, as normally, you have none (you will have one if you have the Giant's Knife).
If you find yourself low on ammo or health remember what you did with Iron Knuckles. Lure Ganon to one of the piles of wreckage and have him hit the rubble with his two daggers. Often times there's a pile of loot to be had underneath.
To get around to Ganon's tail either get him to swing at you and then quickly run around or run right between his legs. Sometimes it's easier to accomplish this by not using Z or L targeting, although it's twice as easy to hit his tail with it on once you get around. You can also hit him in the eyes to temporarily stun him, giving you plenty of time to get around to his backside.
If you find yourself desperatly low on arrows for your bow you can always use your Longshot. Also, on a side note, Light Arrows hurt much more than regular arrows do.
After you've got a couple of hits on him the fire barrier will be removed and Princess Zelda will inform you that you can come get the Master Sword, which is the weapon of destiny and the weapon you must use to kill Ganon.
Once Zelda puts him down, you put him to sleep!
Congratulations, you're done Zelda: Ocarina of Time!
