Early Master Sword (EMS) is a sequence break that allows you to get the Master Sword before completing the Tower of the Gods and the first visit to Hyrule. This is done by activating the cutscene in Ganon's lookout during the second visit to Forsaken Fortress which will give you the Master Sword if you do not have it already.
Because it is not possible to defeat Phantom Ganon in FF2 without the Master Sword, it is not possible to obtain the Skull Hammer early. This sequence breaks can be broken down into 3 parts: Visiting FF2 before beating TotG, entering the Helmaroc fight without the Skull Hammer, and Helmaroc Skip.
Because the courtyard cutscene in Hyrule 2 causes a crash if you haven't unlocked KoRL, you MUST beat FF1 before doing this sequence break. The only known way to skip FF1 is to skip the Courtyard Cutscene using Actor Unloading (note that obtaining the triforce early before unlocking KoRL would skip the Courtyard Cutscene but this is not possible).
You cannot sail in the Forsaken Fortress quadrant if you don't own the Master Sword. To get to FF2 early, you can use superswimming. There is a corner outside the fortress where it is possible to stand. From there, use a wind waker dive to get into the fortress and swim over to the inner-fortress loading zone.
Note: If you save and quit/reset without entering a loading zone in the forsaken fortress, you will be taken to the King of Red Lions who will then automatically sail you back to Windfall. Avoid making this mistake!
Although it is possible to reach Forsaken Fortress a second time via zombie hover from anywhere, this is an extremely long hover that will take at least 15 minutes to complete.
With chest storage, you can climb up the wall before the first sidle gap to reach the door leading to the Helmaroc fight faster, while avoiding the Phantom Ganon fight completely. Since you have chest storage, you can skip the hammer peg by entering Helmaroc early, by jumping behind the door. The deku leaf helps but isn't required. A few different routes are possible:
In order to skip the hammer pegs all around the fortress without chest storage, you can do two different things:
Store the door leading into the Moblin Room. Climb ontop of the grapple spot above the second sidle gap. This will trigger the Phantom Ganon cutscene, but don't worry, you will still be hanging from the grapple spot. Climb up, pull out the wind waker, and immediately cancel it and pull the leaf. The game tried to teleport you back to the door you stored and made you clip OoB. You only have to leaf behind the door and into the loading zone leading to the Helmaroc fight from there.
You can also Zombie Hover directly to the Helmaroc loading zone. You can use the Tingle Tuner to heal, but if savewarp flags are fixed you can also simply die into the loading zone to respawn in the Helmaroc fight.
Right after beating the Forsaken Fortress 1, the game is put either into layer 0 or layer 8 depending if it's the first time you're watching the cutscene or not. On that layer, there are no spikes, no Phantom Ganon battle and no door in the Forsaken Fortress quadrant. This can be used to perform Early Master Sword: simply superswim to FF2 from Windfall and climb the fortress while making sure you are not reloading the area, since that would reset the layers. Once on top of the fortress you can simply walk through the non-existent door and enter the loading zone leading to the Ganondorf fight.
In order to delay beating FF1, you can either perform Outset Escape, or you can skip the Gossip Stone Trigger during your first visit to FF1, which skips having to progress the state of the pirate ship. That way you can go swordless upon going back to FF1 via the pirate ship (only if you've watched the Barrel Launching cutscene), and once swordless, you can get caught by lantern moblins to re-enter FF1 for real.
On the japanese version, playing the Flight Control Platform minigame puts the overworld on layer 1. By playing the Song of Passing on layer 1 you can reach layer 0 and go to Forsaken Fortress 2 where the door will not exist.
See the Helmaroc King page.
Although you will not encounter and problems with getting the Master Sword early at first, there is a major dead end that occurs which prevents you from being able to destroy the barrier leading to Ganon's Tower. Once EMS has been used, it becomes impossible to draw the Master Sword from what is normally the first visit to Hyrule. Though this may not seem important, drawing the Master Sword from Hyrule 1 is one of the flags that triggers the breaking of the barrier cutscene in Hyrule 3.
As such, Barrier Skip becomes mandatory if this sequence break is used.