Final Battle
The Final Battle in Majora's Mask comes in two parts: Entering the Moon, and fighting Majora's Mask itself. The first part offers the chance for the last 4 Heart Pieces in the game, as well as the ability to gain the Fierce Deity Mask for those who have collected all other masks in the game.
Link has gone through a lot in this strange land known as Termina. He has gone back in time more than enough times to give him permanent jet lag, and now he has arrived at the final confrontation with Skull Kid.
If you are completely ready for this battle, go to Clock Town and wait until midnight of the Final Day.
When the clock tower opens, go inside and play the Oath of Order in front of Skull Kid. You will then view a long cut scene of the four giants arriving to stop the moon from falling.
When the mask is revealed to be controlling Skull Kid, it then detaches itself and causes the moon to take on a life of its own. Of course, Link is the hero so he decides to follow the mask into the moon and defeat it once and for all.
Once you have control of Link again, you will find yourself in a large field with a big tree in the distance. Run up to the tree to find five children playing, each one with a different mask on. Four of the children are wearing the boss masks (Odolwa, Goht, Gyorg, and Twinmold), and the fifth is wearing Majora's Mask.
Get The Fierce Deity Mask: If you have all of the masks in the game, you can get the 24th here. You can do that by speaking to the four children wearing the different masks and playing through a very short dungeon for each of them, as well as giving them a certain number of masks (don't worry - you'll get them all back). Also, the final four heart pieces in the game are located in these final four "dungeons".
Odolwa: Deku Link Challenge: The Odolwa child asks for a total of two masks: one before the dungeon and one after. His dungeon is a simple exercise with Deku Link and hovering from flower launcher to flower launcher. You can find a Heart Piece on the far side opposite the exit.
Goht: Goron Link Challenge: The Goht child asks for a total of four masks: two before the dungeon and two after. His dungeon is for Goron Link. This one is tough. Line yourself up along the first path perfectly in the center, and then roll at high speed across the gap. It's tricky: you need to push the control stick straight up to avoid getting off the center line in the beginning (you can manually adjust, but the controls are twitchy). When you get going at full speed, you can release the control stick, and Goron Link will ricochet from chest to chest in a straight line. However after the first few turns, you'll need to make some quick turns manually, until you launch over a ramp to a shrine with a Heart Piece. If you're having difficulties with the second sharp turn, you can actually interrupt the run right before it -- stop rolling -- and line yourself up again for the long straight.
After you get the Piece of Heart, you need to do the initial run one more time. Return to the start and head down the track until you can stop near the center, and cross the bridge to roll across the ramp to the exit. In the 3DS version, the exit is just past the jump after the third chest. Follow the wooden bridge and turn left, avoiding the teleport circle, and roll at high speed to jump to the exit.
Gyorg: Zora Link Challenge: The Gyorg child asks for a total of six masks: three before the dungeon and three after. His dungeon is for Zora Link, and can be tough if you're still struggling with the swimming controls. You need to swim through a large maze with a VERY fast current. In the original N64 version, you get the heart piece take the first left, then the second right, then left again. To get out of the maze take the first left, then the second right, then straight.
Twinmold: The Twinmold child asks for a total of eight masks: four before the dungeon and four after. The final child sends Link through battle after battle against familiar enemies. If you use your Great Fairy sword, most of them will fall pretty quickly:
Room 1: The first room only contains some bottles.
Room 2: You will fight a Lizalfos in here, one hit from the Great Fairy's Sword will do him in.
Room 3: Nothing but a Gossip Stone.
Room 4: The battle here is a Garo Master. Defeat him the same way you did in the one of the Stone Tower and then use the Hook Shot to reach the chest above.
Room 5: see #3.
Room 6: You'll fight another Iron Knuckle in here, and get Bombchus as the reward. Look at the wall and release a Bombchu so that it explodes on the crack, then shoot the switch to make a ladder appear.
Room 7: Look to the ceiling and again release a Bombchu so that it will explode on the crack to open the door and give you access to the end of this dungeon.
In the 3DS version, simply shoot a fire arrow at the frozen eye on the ceiling to open the door.
Once you have played with the four children (and given up all of your masks except for your transformation ones), speak to the child wearing Majora's Mask to receive The Fierce Deity's Mask. Then agree to "play" with him to be taken to the final battle.
FINAL BOSS: Majora's Mask
There are two different ways to defeat Majora's Mask; the easy way and the hard way.
The easy way is to put on the Fierce Deity's Mask, Z-Target the boss, and just slash away until it is dead. Fierce Deity Link's huge sword does massive damage, and will also shoot bolts of energy from extreme range. He'll only be slightly stunned or damaged by anything Majora can produce, so keep the hurt on and Majora and all of his forms will fall fast.
The hard way is for those who did not bother to get all of the masks in the game. You should make use of all the bottles and have several fairies, blue potions, and a bottle of Chateua Romani.
Majora's Mask
Majora's Mask has a couple forms.
The first one is the mask itself, and it can only be hit from the back.
This form will move around the room, trying to face you at all times to keep its back protected. You can counter this by using Zora Link's boomerangs to hit it from the back. When it gets hit, the mask will fall to the ground stunned, where you can attack it some more. The Great Fairy Sword is useful here, but remember to swamp back to your Gilded Sword and Shield to be able to quickly defend. After taking some damage, the four temple guardian masks will emerge to attack you as well, shooting bolts of energy from all sides. Take them out with a few arrow shots each, so that they will not bother you for the rest of the fight.
Majora's Mask will also attack by spinning around the room and trying to ram you, or firing a laser beam directly at you. To counter the first attack, turn into Deku Link and burrow into a hole at the center of the arena, and launch out when he spins past. To counter the laser, use your Mirror Shield to reflect the laser back at him.
Majora's Incarnation
When the Mask spouts legs and becomes its next form, Majora's Incarnation, use arrows to stun it, then run in and slash it with your sword. Keep your shield to block its attack. It can be difficult to hit as it runs extremely fast and dodges constantly. You can also use Zora Link's Boomerang to chase it as it taunts, or roll around as Goron Link and ram him to knock him to the floor. Keep damaging the incarnation every time it falls over, and you'll head to the last part of the fight.
Majora's Wrath
The final form, Majora's Wrath, is a stronger version of the previous one, and this one has whip-like tentacles. Keep it Z-Targeted, and stun it with an arrow, if possible. Zora Link can be extremely useful here, as your barrier can stun Majora's Wrath, and allow you to get in close without taking too much damage. When Majora's Wrath tries to latch on to you with its whip arms, you can use your barrier to send an electric shock back at him, and then run in with the Great Fairy's Sword to maximize your damage.
The Ending
The final sequence of Majora's Mask will vary depending on how many masks you collected throughout the game. If you got all of them, you will not miss anything. If you missed a mask, you will just see it rotating as the sequence that it unlocked plays out behind the black screen.
Congratulations, you have beaten The Legend of Zelda: Majora's Mask. If you got Oni Link, and you want to have some fun, you can go back in the game and beat up any of the bosses with that awesome sword of his! Just remember to bring Green Potions, because his sword uses up alot of Magic!