The Legend of Zelda: The Wind Waker/Ganon's Tower

Ganon's tower is short but rough. There is a few things that you need to do before you go up against the trademark villain you have to defeat to finish this story.

Castle Basement
Remember where you left Tetra or Princess Zelda? She turns around and disappears in a flash of light. You'll hear Ganon's voice, telling you that he has captured Zelda and you have nowhere to run. You'll be surrounded by a ring of flames and you'll face two Mighty Darknuts. Keep moving, sword ready, and parry at the right moment. Once you finish with them, the fire disappears. Go out, not where the King of Red Lion is but where you encounter the barrier. The first time since the sword is dull, you can't break through the barrier. This time you can so just slash and the barriers break. Along the way, you fight Peahats, Red ChuChus, Moblins and a Mighty DarkNut. Shoot your hookshot at the targets and watch out for Keeses before you head into Ganon's Tower.

Black and white boss rematch
This part is similar to Ocarina of Time in which you need to solve all the puzzles before you go into Ganon's Tower. Here's a quick rundown: Note: If you have hero's charm, you can tell in all but Ganondorf has the red bar telling you how far from defeat has come to the bosses. Also the Tower of the Gods boss is not there because they're not under the influence of Ganondorf so their dungeon that supposedly stripped down is nowhere to be seen. Once you beaten all four rooms, the door would be unlocked.
 * In Dragon Roost Cavern Room, there's two ways to get across. Below, you use your ice arrows to avoid the red bubbles as you make a path across the lava. The other is using the grapple hook. Where you reach the end, use the deku leaf with enough height to get across the lava to the boss door. You're going to beat Gohma again in black and white with warbly music. Your master sword should make quicker work than before but your inventory has been stripped down temporary until you finish the boss. So equip the grapple hook, and swing Valoo's tail three times to crack the shell. Then pull his eyes and finish him off around two times.
 * In Forbidden Wood Room, you need to use the deku leaf extensively. Bring the platform by blowing the pinwheel. Then as the snake like platform drops, drop to the spot with the deku leaf and do the same with the second one. Then glide to where the boss door is for another fight. You're going to fight Kalle Demos in black and white and again your inventory is slightly stripped until the boss fight ends. Equip your boomerang and repeat this pattern: Target as many vines as you can. As soon as the petals drop, attack the centre flower.
 * In Wind Temple Room, defeat the Wizzrobe with your arrows, then glide across the room using the springboard as your launching pad. Once you reach the end, hookshot to your next battle. Molgera is being tough once again in black and white, with your inventory lightly stripped. Equip your hookshot and repeat this procedure: Aim for the middle part and also take care of his minions as well.
 * In Earth Temple Room, the first part is rolling across the falling crypts up the stairs. The second and third part is getting the purple ChuChu's stoned and putting it on the pressure switch to get to the stairs after you allow more crypts to drop. The third part near the end is a Stalfos but ignore him because of the final fight. Jalhalla should be fairly easy to beat in black and white. Your items has been taken off but you have your mirror shield. The first part using the lights and mirrors to stun him and throw him to the very spikey column. Then cut down on his poes. The second part is harder as there is one light is randomly moved at a time and you need to manually aim at the boss. Repeat that process until he's finished.

Torches and Crystal Switches
You think you're near the end, but there's still more that needs to be done. So go up the stairs and take care of Miniblins. In the large round room, go through the door on the entrance right. The camera will at four torches in this order. The King tells Link through the gossip stone to remember every detail in the room. There's a tablet that reads "The sword hilts of my servants who lurk deep in the darkness shall be the guideposts that point to me." Remember this for the very next section. Now go to the opposite end, which is the left entrance with the switches. Follow the order in the same way with the torches. Stand in the middle and equip your boomerang. Now follow this order: far right, near left, near right, far left. A simpler way is middle right, second left, second right and middle left. The best interpretation is in number from 1 to 4: 2 4 1 3. So choose which method works for you. This opens the portal between here and Forsaken Fortress.

Note: If you need to go out and do something, do it now. When you come back, warp to Windfall Island and sail to Forsaken Fortress when you finish. Don't warp to Mother and Child Isle where you can gather up fairies but then the only way is to warp out. Don't visit Mother and Child Isle unless it's important.

Phantom Ganon Puzzle Quest
When you're done with unfinished business, go back here and run back to where the torches are and jump in where you warp into the Phantom challenge. There are a few variations with Phantom Ganon. First is hitting the white electric ball with your sword like a tennis ball. Second is the four Phantoms and Third is the clusters which you could hit back with your sword. Once the sword drops follow the swords hilt. Not the swords edge or you'll either have to deal with Moblins or you'll warp back and you have to start again! To be clear the swords hilt is where you hold the handle. It will take seven Phantom battles - assuming you made the right choice! A chest appears at after the seventh fight. As you open it you get the Light Arrows. Now go through the other door where the sword hilts point and you'll warp back where the four torches and four switches are at the entrance. For the final Phantom fight, take out your Light Arrows and take one shot at him to finish him off. Then take the Phantom Ganon's sword and throw it through the door you haven't gone through which is the horn-like sigil sign. Go up the stairs taking care of all remaining enemies which is three Moblins, a Darknut and two Mighty Darknuts. Defeating all enemies unbars the door at the stairway's top.

Puppet Ganon
The cutscene once you go through the door is Ganon piercing into Zelda's dream and deciding to give you a dangerous showdown by turning into an enormous Moblin (really a Puppet Ganon) for you to fight.

Puppet Ganon has three stages: humanoid, spider, and snake. To beat the humanoid Puppet Ganon, use the boomerang to sever all of his blue strings (the red center one cannot be severed). The strings will take multiple hits before they fall. While Puppet Ganon is vulnerable in this position, shoot the glowing blue crystal on its tail with a light arrow. Shoot the tail with three light arrows to go to the next stage.

In the spider stage, Puppet Ganon retracts into the ceiling and spins around. Use his reflection in the pool on the floor to see where he and his blue crystal will land. Position yourself so you can shoot the crystal with a light arrow when he comes down. Alternately, wait until the spider stops spinning at the top of the room, aim upwards with a light arrow, and shoot while the spider is falling. This way helps you avoid damage in general, and makes this part of the boss much easier if you have a good aim. Three light arrows will put an end to the spider.

Finally, in the snake stage you must avoid Puppet Ganon as he rampages rapidly around the room. It's best to find a way to get up on the wood platforms high above the ground.(You may have to move a bit while targeting, because the monster hits the walls)You must shoot the blue crystal three times to rid yourself of Puppet Ganon forever. Shooting the snake's head or hit him with the sword will stun him, but only briefly.

Note: Make sure your jars are filled with grandma's Elixir and either fairies, red, green or blue potions as they're needed for your health, magic and importantly your light arrows. Also, be prepared to manually shoot the blue round crystal at a moments notice depending on which stage are you in. Lastly, upgrade your arrows and magic meter or you'll be shortchanged in this three part boss fight!

Ganondorf
Ganondorf, with the unconscious Zelda, compliments Link before he disappears. Now, you can choose to go back and do anything that needs to be done and also save so that you won't have to deal with Puppet Ganon again. Here's what you need to do if you want to end it once and for all. Jump on to the Puppet's red string to climb up to the top, holding. Once you reach the top, hop onto the center of the platform, then go near the platforms edge at the opposite end of this section. Grapple and climb up further to the top. The center of the next part has jars for you to break, so smash them to recover health and magic to help recharge Link to full strength. You can use warp so the jars can appear and you can collect as many as you want until you're satisfied. Now find the red entrance with the blue doorway and hookshot to the target for the final platform.

The cutscene is simple: Ganondorf knocks Link unconscious, the King of Hyrule makes a final wish by touching the Triforce and Ganondorf finally rages on Link in a final showdown!

In Ganondorf's first stage, you cannot hit him normally. You must wait for him to attack you and then parry his attack to stun him. Once he is stunned, you can hit him from behind with the Master Sword. Meanwhile, Zelda runs around the room shooting Ganondorf with light arrows. When the second light arrow hits, the second stage of the battle will begin with a cut scene of Ganondorf knocking Zelda over. The second stage is fought exactly like the first stage, except Ganondorf's attacks are more vicious. After a few hits, Zelda will wake up and tell you to distract Ganondorf. This is the beginning of the third and final stage. Zelda will shoot at your mirror shield with a light arrow and you must reflect that arrow back at Ganondorf. When that attack connects, Ganondorf will be stunned. Then do the final blow as the button flashes, press it for a final attack.

A final set of cutscenes shows Ganondorf's demise, the King of Hyrule's actions, and lastly, Link and Zelda floating up to the surface as Zelda reverts back to Tetra, with Prince Komali flying overhead. They follow a ship with Aryll wearing different clothes before the credits. The last part is Tetra and Link with the King of Red Lions sailing off with Aryll waving goodbye.

You can choose to save over your file or not and you'll unlock the second playthrough with many surprises to be expected, if you want to play it again.

Special note: If you're expecting a sequel, think not. Get a DS if you want to play The Legend of Zelda: Phantom Hourglass and The Legend of Zelda: Spirit Tracks to see what happens to Link after this game.