In his puppet form, the monster is hanging from the ceiling by several strings. Use the Boomerang and cut the strings if possible in two hits. Once all the strings got cut, his tail will hit the floor. Shoot a Light Arrow at the blue pearl at the end of his tail and he will climb back on the ceiling. Do this twice more to beat him (for the time being). Get rid of the Keeses to refill a few hearts and your magic.
In his second form, he will look like a spider and fall from the ceiling. Take a look at the ceiling to know from which side his tail will fall, then as soon as he stops, rush to him. When he falls, shoot another Light Arrow at the pearl. Clear out some Keeses from time to time to refill your magic. Do those actions twice more to defeat him.
In his third form, he will look like a caterpillar, and quite a fast one! If you have a swift eye and great reflexes, you can hit the pearl on his tail while staying afar. Otherwise, you can strike his head with your sword to stop him for a few seconds, but you still have to be quite fast to hit his tail with a Light Arrow. When you touch him three times, Puppet Ganon is vanquished!
Ganondorf will invite you to get on the roof to confront him. Get on the platform in the middle, then jump on the red rope to grab it. Climb to the top, then use the Grappling Hook on the wooden bar (between the two lighter parts) and climb the rope. Break the pots to get a few hearts and ammunitions, then use the Grappling Hook again to reach the upper level. Clear the way to the warp pot and break the pots to get (among other things) a small fairy. Get close to the window, then while staying right in front of it, shoot the Grappling Hook at the target in the middle and get out.
The Last Stand
With Zelda sleeping and Link passed out, Ganon will unite all three parts of the Triforce. But the King of Hyrule intervenes right on time to avoid the worst and asks the Goddesses to flood Hyrule to allow a new hope to emerge. But this isn't the end for Ganondorf...
Wielding two swords, Ganondorf is quite difficult to reach. During the first phase, Zelda will shoot Light Arrows at him. As soon as he gets struck, dash towards him to swing your sword a few times. After a few hits, Ganondorf will throw Zelda to the ground and the second phase will begin. Stay away from Ganondorf, use the L lock and when you see him jumping to hit you with his two swords, press A to get behind him (the button will turn into a star) and strike him a few times. Repeat this tactic a few times more, then Zelda will get back to her senses.
During the final phase, Zelda will shoot Light Arrows at you so you can deflect them with your shield at Ganondorf. Try to stand so that Ganondorf stands between you and Zelda, then when the Princess draws her bow, use the L lock, raise your shield and get close to Ganondorf. As soon as he gets struck, strike him. If he received enough light, the A button will turn into a star, this is the time for the final blow!