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 loading zone by clipping out of bounds. There are three different ways to do it. The original method uses a Ledge Clip. It was more recently discovered that it is possible to use a Roll Clip to do the exact same thing.
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 using an Item Slide.
It is a common misbelief that you need to tap towards the wall on the control stick to move towards the wall. Do not do this. For Ledge Clips you will always tap away from the wall you're trying to go through. The item in turn then pushes you through the wall.
There is an older tutorial for this trick that uses the opposite ledge than shown in the video above. If you choose to follow this tutorial you can ignore the part about leafing between the pillars in the room and just Item Slide to the door frame in question.
You can use a bomb to push you far enough in to the wall for you to do a roll clip.
1. Kill the bokoblin.
2. Dry Roll and Ledge Hang off the edge to your left.
3. Climb up and pull a bomb, then drop it with B after it is fully above Link's head.
4. Backflip and pull the leaf once you are at the same level as the ledge.
5. Grab the ledge between the wall and the bomb.
6. Do a partial Ledge Clip as soon as possible and then climb up the wall and perform a Roll Clip to the left.
8. Leaf Pump to the loading zone as need be.
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.
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.
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.