The Legend of Zelda: The Wind Waker

He's at the very top of Ganon's Castle.

You have to defeat four bosses then go through a puzzle of doors to find him.

I need more than that is he in hyrule or the under water castle at the forsaken fortress

Give us more info than just that. It's hard to give exact help when one does not understand the question enough.

He's in Ganon's Castle. you have to kill the four black and white bosses then go through a puzzle involving phantom ganon.

................You need to get all triforce pieces then beat the earth wind temples then go to his castle beat the beast the he changes into. the climb the rope the the top from there use the graplinghook then you fight him again. when you get all triforce pieces somthing should happen.

You're in Ganon's Castle? Where in it might help, but I'll just do this.
When you enter Ganon's castle, You have to treat it like just another Dungeon/Temple. This time though, Ganon is the final boss.
You will come in and you can go in 5 different directions...avoid straight, and do the four kiddie corner doors. You will go through small puzzles in each, and at the end of each, you will have to re-fight one of the four main temple bosses. Gohan, Kalle Demos, Jalhalla, and Molgera. Once you beat all four, you go on that straight path, up the stairs, and go right. You will find yourself in a maze with phantom ganon. Beat him the first time, and go through the door that the fallen sword's HILT (the handle) points to. then after that, Ignore phantom Ganon and go: left, straight, left, right, Straight, straight. In that room, Fight Phantom ganon again, and get the light arrows. You will be returned to the room before the "maze" and you will fight phantom ganon one last time...except this time, one light arrow will do the trick. Pick up his sword, and slash the wall with the fancy character on it. Go up the stairs, taking out enemies all the while...then you need to fight puppet ganon. Beat him, and climb his rope. Then use your grappling hook and hookshot to climb higher and higher until you see a door...go through, and there's ganon.

in Gannon's Tower you have to defeat the four bosses you defeated previously only now you have the master sword and they are in black and white. after that you have to go to a room that has two doors go to the one on the right watch the cut scene and then go to the other room and hit the unlit torches in the order they zoomed in and then king of red lions will show up and ask if you want to do something before you go further. If you have nothing else to do go to the other room and jump into the black ness. you then have to defeat the phantom Gannon then look at the sword he was holding and go through the door the handle is pointing (otherwise you will have to do it again.) then you will have to do that 7 times and you will then get the light arrows and will end up at the room with 2 doors that work and you will have to fight another one but this time you have the light arrows.go through the door defeat all of the enemies and go through the huge red door and you see Gannon and Zelda( AKA Tera) then you have to defeat all three stages of puppet Gannon and then you climb the rope and then you go all the way to the top and then fight Gannon.

Inside Gannon's tower there are two parts the first part is long you have to defeat four bosses you fought before but it's different you can only use the weapon that is needed for the boss battle but the fights the same if you already did that then go through the door straight with a skull lock after that there are three door's in front of you the one straight leads to gannon but you can't get there yet. the door on the right when you go in it show's an order memorize it and go to the door on left and hit the candle in the order and the king of red lions will show up and a portal this is if you want to go back . Go back to the other door and drop down trust me just do it. Now when you drop you will drop to a maze and you will have to face shadow gannons i recomend you dont fight them because then you will lose which door your supposed to go into the order is left,straight,left,right,straight at the end you get an AWSOME item kills any non boss in one hit but i wont tell you what it is. now if you dont under stand go to www.gamefaqs.com/console/gamecube/file/469050/22209 and that might help you

First beat the phantom gannons and go to the rooms that the bottom part is pointing to then you get the golden arrows
you end up fighting 1 more phantom ganon and when you beat that phantom Ganon you pick up its sword and
swing it on the door thats locked keep going forword and you'll find puppet gannon then after that you climb up those
things and beat the last gannon.

First beat the 4 bosses which you beat only revived then beat those devils. In the next room, you have to solve 2 puzzles. On the left, you have to use your boomerang but you can't open the {spoiler alert!] portal so you have to go to the other room on the other side. They'll show you the correct order to open a portal to Forsaken Fortress. They'll review the order in room where you have to use your boomerang. The King of Red Lions to come in. On the right room, where you figured out the portal puzzle, you have to JUMP into the hole in the middle. The clone Ganondorf should appear and attack you. You have to go through random doors. But if you go through the wrong door, you have to start again. Don't worry! The order for the doors you have to go through stay the same. Every time you go through the correct door, a new clone will appear. Keep going through the CORRECT doors and you'll find MAGIC ARROWS! Use them to beat a clone when you return at the middle of Ganon's tower. After, use the clone's sword to blast the door. There are monsters and lots of bosses ahead. Be careful... P.S. Ganon turns into puppet forms.