Once you obtain the remains of the four bosses, you now meet the requirements to complete the game. Complete all sidequests at your leisure, using the Song of Time to restart as necessary.
As with the beginning of the game, you need to arrive at the Clock Tower within the final six hours. To skip forward to the final night, play the Song of Double Time.
Initially, you needed to collect the Moon's Tear to reach the tower. Now that you're Human Link, you can simply walk up a small ramp from the side and climb to the entryway.
In this encounter, you have a chance to change the result. Play the Oath to Order, and the moon will be stopped.
The moon appears as a plain of grass, with a lone tree in the middle.
You can speak with the kids running around the tree and give them masks. When you speak with them, you can give non-transformation masks to enter a trial, in which you'll have to complete a small challenge to find the kid and, optionally, collect a Heart Piece on the way. When you find the kid, you'll have to give him more masks to be returned outside. Every trial also contains several Gossip Stones which, when read with the Mask of Truth, reveal the locations of all the masks in the game.
You cannot give the Deku, Goron or Zora Masks.
Give the kid wearing Odolwa's Remains one mask to enter.
Put on the Deku Mask and fly to the first spinning platform. The next jump needs to be timed carefully; at the second spinning platform, there's a normal and a yellow Deku Flower, and you will need to land on the yellow one. Additionally, there's spikes which knock you down into the abyss. Land on the platform after one spike has passed, then quickly burrow into the flower before the next one comes. Fly to the top right corner to reach a Piece of Heart, then return to the spinning platform. and fly to the other corner to find the kid. Give him another mask to return outside.
Give the kid wearing Goht's Remains two masks to enter.
You'll need to roll straight forward as a Goron to make it through the maze. This looks difficult, but can be made super easy with a little trick: roll forward, and behind the first set of chests step on the beam thingy, which will return you to the beginning in just the right position. Curl up, roll forward and release the control stick once the spikes appear to make it all the way through.
After a while there will be no more chests at corners, and a bridge will branch off to the right. If you wish to get the Piece of Heart, use the control stick and keep rolling down the path all the way to the end. Otherwise, cross the bridge and roll towards the ice platform you can see in the distance to get to the kid. Give him two more masks to return outside.
Give the kid wearing Gyorg's Remains three masks to enter.
Put on the Zora Mask and dive in. This is a maze of pipes. To find the Piece of Heart, go left, right, left and left. To find the kid, go left, right, left and right. Give him three more masks to return outside. Every other path will lead to a Gossip Stone.
Give the kid wearing Twinmold's Remains four masks to enter.
This is a little dungeon, and you'll have to beat an enemy in every other room. First off is a Dinofol, who is really easy with your new weapons. (He dies to one single slash of the Great Fairy's Sword!) After a Gossip Stone, you'll face a Garo Master. Defeat him just as you did in Stone Tower Temple, then hookshot up the chest.
In this Gossip Stone room, you can utilize a very useful trick: play the Song of Storms and go to the next room. The ladder, which would normally have to be revealed with a Bombchu and an arrow, is now already there, so you just need to kill the Iron Knuckle to progress. Get the Bombchus from the chest that appears, then go to the next room. Pick up the Piece of Heart in front of you, then look above to see a crack in the ceiling. You'll need to time the Bombchu so it explodes right at that crack, which will reveal a frozen eye switch. Use a Fire Arrow to hit the switch, which unlocks the next door. This leads to the kid, give him your last four masks to return outside.
Once you're done, speak with the kid sitting in front of the tree wearing Majora's Mask. If you gave away all your masks before, you'll get the Fierce Deity's Mask, one of the most powerful masks. In any case you'll be brought to the room of the last boss in the game.
Step forward. The bosses' remains will leave you and attach themselves to the walls, after which Majora's Mask will awaken and start the fight. He has no real attacks aside from spinning around wildly across the battlefield. You'll need to stun him either by shooting arrows at his back, or by simply using Zora Link's boomerangs. Afterwards, strike him in some way and repeat the procedure.
After a few slashes, the four remains will awaken to join the fight. They shoot energy balls to hurt you, and stay throughout the fight, so you may want to get rid of them so they stop being a nuisance. Majora's Mask will start using a fire beam at this point - with the Mirror Shield, you can deflect it right back to him and damage him. After a few more hits, he will progress to his next form.
Majora's Incarnation does nothing more than running around and very occasionally shooting energy balls at you. There are two ways to deal with him: you can try stunning him with an arrow and then attacking him (which is a bit difficult due to his sheer speed), or transform into Goron Link and roll around akin to the battle against Goht.
After a few more hits, he will transform to his final form.
This is quite difficult. The two whips can hit you wherever you are, and he jumps around the battlefield all the time. Just before he attacks, shoot a Light Arrow to stun him, then quickly get a few hits on him before he gets back up. After a few hits, he will start creating explosive spikes that try to hit you and then explode in your face. Keep your strategy going to hopefully defeat him. Once he has died, enjoy the credits!