You should have everything else done at this point of the game; 7 Bottles, 19 Heart Containers, and 23 Masks.
Start your preparations by going to the Latte Milk Bar and buying Chateau Romani for 200 Rupees. Drink it for unlimited Magic then collect 7 Fairies, the Southern Swamp has some right next to the Owl Statue as does Zora Cape.
The only thing left is to stock up on Arrows and Bombs, so purchase some or collect some then head to the top of the Clock Tower at 12 AM on the Final Day.
The battle against Skull Kid commences like it did the first time, but this time you already have the Ocarina of Time so play the Oath to Order and to trigger a lengthy scene where Link winds up on the Moon.
You start in a green pasture with a large tree in the distance, run to it to find four children wearing masks of the four bosses you fought.
These children are running around but a fifth is seated with Majora’s Mask on, speaking to this one starts the final battle but you’ll want to speak with the other children first.
Speak with the Odolwa Child and hand over 1 Mask .
In this miniature dungeon you’ll need to use the Deku Mask and the Deku Flowers to fly to spinning platforms in the middle.
Navigate to the northeast corner of the room to find Piece of Heart #49 then exit at the northwest end. Speak with the Odolwa Child again and hand over 1 Mask to leave.
Speak with the Goht Child running around the tree and hand over 2 Masks .
In this next dungeon you need to use the Goron Mask. Charge up and roll into the chests at the intersections but release the Analog Stick so that you bounce perfectly toward the next chest.
At the midway you can see a large turn and narrow bridges leading to a central area, stop here. Leap over to the snowy platform and go through the door to find the Goht Child but turn around and exit. This now serves as your restart point should you fall.
Head back to the central platform and off to the path once more. Continue rolling and bouncing off the chests to reach the end of the road where Piece of Heart #50 awaits. Exit back to the Goht Child and hand over 2 Masks to leave.
Back at the tree, speak with the Gyorg Child and hand over 3 Masks.
The next area is a series of paths that are opened via Crystal Switches. This also means that it’s timed and it can be a little difficult and frustrating if you fail a few times.
Start by diving and hitting the Crystal Switch, then continue down the pipe while using Electric Barrier (you do have infinite Magic if you used the Chateau Romani as instructed). The path splits and you want to go left.
As you reach the platform you need to continue using Electric Barrier and launch out of the water and up onto the platform. Poor timing will leave you short and through an empty pipe which sends you back to the start.
The next area is much the same, hit the Crystal Switch and at the fork go right then up to the next platform. The final area splits top, middle, and bottom instead of left, center, and right.
Hit the Crystal Switch and take the middle path to find Piece of Heart #51. You’ll have to start all over again, but take the top path when you want to leave. Give the Gyorg Child 3 Masks to exit.
Speak with the Twinmold Child and hand over 4 Masks.
This is basically a Mini-Boss dungeon, the first room is a Dinolfos. The second room is a break, the third is a Garo Master! Hookshot to the chest that appears once you defeat it and head to the fifth room. Here, use the Great Fairy Sword to defeat the Iron Knuckle.
Open the chest to get some Bombchus. Look at the wall to your right and notice the cracked portion, release a Bombchu after 3 ticks from the middle of the room towards the wall and you’ll blow it up. Shoot the eye switch then climb the ladder that appears.
In this next smaller room release a Bombchu up the wall so it explodes on the ceiling, revealing a frozen eye switch. Grab Piece of Heart #52 and make your exit, speaking with the Twinmold Child and handing over your last 4 Masks.
The Fierce Deitys Mask
If you’ve completed the other four mini-dungeons then the Majora Child will give you the Fierce Deity’s Mask. This mask is incredibly powerful and can only be used during Boss Battles (and Fishing!).
Speak with the Majora Child when you are ready to start the final battle.