Go through the door and kill the torch slugs.  Use a spin slash to trigger the first shock switch, which makes a chest drop containing Bombchu's.  Use a bombchu on the fence to have it climb up the fence, go through the hole up there, then climb down the other side to finally blow up the second shock switch (good use for a bomchu eh?).  Go through the door now and through an entryway to a room with some sun symbols on the wall.  Shoot the hole in the ceiling with a Fire Arrow to let in the sunlight.  Use your Mirror Shield to reflect it onto the symbol just to the right of the entryway (NOT the doorway!) to unblock the door.  Go on to the final floating ball thing.  Kill it with a Light Arrow.

Now leave Gannon's Castle to stock up.  Use the Great Fairy's fountain to heal your life and magic.  Make sure you have at least 1 blue or green potion because you may need it to refill magic during the final battle.  Fill the rest with faeries.  Also be sure you have a full quiver of at least 40 arrows.  Now go back into Gannon's Castle and go into the tower in the middle of the room.  Go up the stairs and through the door.  Now you'll just have to keep killing all the enemies in the room to unblock the next door, then go through and up more stairs.  About halfway up you'll find the Boss Key in a chest surrounded by fire that you need to kill all the enemies in the room to get to.  Eventually you'll also have to fight two Iron Knuckles at the same time.  Don't worry though they're slow enough you can just work on one at a time.  Remember to wait until they get close enough to swing, then backflip with back+A, then push A again when you land for a jump slash.  Once you've climbed enough stairs you'll end up in a huge room with a giant pillar in the middle of it and pots everywhere.  Don't break any pots; you'll need them later.  Find the other door and go through it and up a huge flight of stairs.  You'll pop in on a small story sequence when you go through the door the top.  Afterwords you'll face the big guy himself, the Evil King....

The Final Boss: Gannondorf

Immediately put on your Hover Boots and run to one of the corners of the room.  Now face Gannondorf, tap Z to center the camera, and wait until he throws a ball of lightning at you.  Remember Phantom Gannon?  Hit the ball to reflect it back at him and be ready for when he knocks it back at you.  Keep hitting it until it hits him.  He'll be stunned for a second, so take this opportunity to shoot him with a Light Arrow.  Turn run over to his platform, Z-target, and wail on him with your sword.  When he gets back up quickly run back to your corner.  If you fall off, break the pots to get some life/magic/etc. and then use the Longshot on the side of the middle pillar to quickly get back up.  Then as soon as you climb over the top, turn to face the nearest corner, tap Z to center the camera, and run over to it before he knocks you back off again.  After a while he'll try a more powerful attack.  When you see him start gathering a big dark ball of energy above his head, hold down B to start charging a spin attack.  When he lets it go it will fire 4 lighting balls at you. Release the spin attack to reflect all 4 back at him.