The second room in Ganon's Tower consists of four doors each leading to a different trial, at the end of which you need to refight the boss of that area. You are supposed to refight all four bosses to break down the stone wall blocking the loading zone to the next area. It is however possible to skip these trials and go right to the lading zone by clipping out of bounds. There are three different ways to do it. The original method uses a bomb ledge clip. It was more recently discovered that it is possible to use a roll clip two different ways to do the exact same thing. All three of these are possible on both The Wind Waker and The Wind Waker HD.
This was the first method of skipping the trials that was found, although it used a frozen bokoblin instead of a bomb which is way more difficult. To do this ledge clip you need to make your way over to the door frame as shown in the video.
It is a common misbelief that you need to tap right on the control stick to move towards the wall. Do not do this. For a ledge clip, you will usually press towards a bomb or whichever item you are using. The item in turn then pushes you through the wall.
A roll clip to skip the trials from the lower level is possible with nothing but the Deku Leaf. To do this you need to grab the ledge so that practically all of Link's left hand is in the wall.
Optionally, you can tap down on the c-stick at some point before cancelling the leaf for the ledge grab to make it easier.
You can use a bomb to push you far enough in to the wall for you to do a roll clip. Do note that this is significantly harder than the bomb ledge clip. If you wish to use a roll clip, it is recommended that you use the alternate (bombless) roll clip method. However, in case you wish to try this, here is a video and a brief description of how to do it.
Once you finally skip the trials, you will be on a staircase that has miniblins spawning at the top. Climb it and go through the door to make your way towards the tower's second section. You can also sidle on the side of the door to trigger the loading zone and skip opening it which is frames faster.
Once going through the loading zone, you will be in a room with two doors and another stone wall that looks like it can be broken down. It can. Through the left door is a room that allows you to spawn a warp portal to the Forsaken Fortress provided you have the boomerang. It also "spawns" the King of Red Lions which you use to go back and forth through said portal. Funnily enough, the King of Red Lions is already spawned, but waiting out of bounds for you to hit the switches. With cheats you can get to him while out of bounds and do some silly stuff. If you wish to see this you can click here.
The door to the right is the path you need to take to get the Light Arrows. It is possible to skip these and we will go over that shortly. Once going through the door a short cutscene will play showing you the lights on the wall in a specific order. This is the order you would need to hit the switches in the other room to trigger the warp. Anyway, to continue towards the Light Arrows, jump down the pit. You can pull the Deku Leaf while over the pit to trigger the loading zone faster.
Upon the next area loading you will find yourself in a maze. The maze is the same every time so it is to your benefit to remember the directions for it. They are as follows...
When going through the final (6th) door, you can use a bomb pull before opening the door to skip a cutscene on the other side of the door as it bars itself shut behind Link. For more on that click here.
In this room you will fight Phantom Ganon for the Light Arrows. The fight is very short and extremely easy. He has three different attacks. He can throw a white orb at you, a red orb, or he can spawn all around you with four clones. If he spawns in the air he will be using either the white or red orb. If he spawns on the ground you will know it.
If he spawns in the air and goes to throw a white orb at you, get as close to him as possible before he throws it. If you are close enough you will only have to hit it back once for it to stun him. Simply slash him as he falls to the ground to kill him.
If he spawns in the air and holds a red orb above his head, charge a spin attack by holding B. When he throws the orb it will break in to eight smaller orbs. Release your spin attack when they are all about to hit you so they all fly back to him. Hit him with your sword when he falls to the ground to kill him.
If he spawns all around you with his clones, simply hit the one that spawned behind you. The real one will always spawn behind you so it is best to stand still once you walk forward a little bit. Hit him again to finish him off.
Open the chest for Light Arrows. Go through the door that opens to head back to the main room for this area.
In the main room at the beginning of the Phantom Ganon battle, preform storage. Attempt to open the door on the left of the central door that leads to the grand staircase. The door will not open and you will have stored it. Head to the opposite side of the room and open the door. Now return to the previous room. You will notice that the door the you tried to open with storage activated is now open. Jump through it and glide to the loading zone.
Head over to the room on the right that leads to the Phantom Ganon battle and wait for the cutscene to finish. Head over to the left near the drop off by by the stone. There is a little indentation which when you run towards will allow you to jump without falling into the Phantom Ganon battle. Once you have found this spot, run off it and use the deku leaf to get on top of the stone.
Set a bomb down and then pull out the wind waker and cancel it so that it is still in your hand. Now here comes the tricky part, getting a wind waker dive off of the bomb followed by dry storage. Sometimes you can simply flick the control stick towards the bomb at an angle and mash the button your wind waker is on to get the dive. Once you have gotten it, cancel the wind waker just in time to get dry storage (pause buffering may help with this).
Store the text from the stone and run back over to the door. As you press A to open the door, the text from the stone will pop back up. Quickly mash through the text box to keep the door from closing. Now run over to the door on the opposite side of the room, watch the cutscene, and return to the preceding room. Run through the open doorway and leaf pump to the loading zone.
Note: Because of the difficulty of Puppet Ganon Skip, this is most likely TAS only, or for use in a segmented run.
At the very top of the grand staircase, align with the pillar on the left as shown. Backflip and pull out the deku leaf. Just as you are about to hit the ledge, put the deku leaf away to grab it, and shuffle your way as far to the right as you can go. Now climb up the ledge and immediately jump towards the wall to clip through it. If you wait to long Link will simply fall off the ledge and you will have to start over. From here, make your way to the loading zone, being careful not to fall.
In Puppet Ganon's chamber, angle yourself towards the path that leads to Ganondorf. Deminish you health to 1/4 heart and zombie hover. This is a mostly luck based hover, as the conditions have to be perfect in order to prevent from getting knocked down by the Keese. Once you are above the red wooden entrance to the Ganondorf battle, wait for a few Keese to come and attack you. Equip the deku leaf and bombs. Quickly press the button the bombs are on, followed by the deku leaf, then B. If done correctly, you will drop a bomb and get a heart drop from the Keese.