The First Three Days
As soon as you enter the town, The First Three Days will commence. Tatl will tell you to go to the Great Fairy who is located in North Clock Town. To get there, run around to the back of the clock tower, and you will find an entrance to North Clock town.
The Great Fairy's room is located up the small ramps at the far end of the area. When Link enters the center of the room, he will be told to locate the one missing Fairy in Clock Town and to return it to the fountain.
To find it, run through East Clock Town until you get back to South Clock Town. In the corner directly across from where you enter, you will find a small ramp that leads to an exit, go through there to arrive in the Laundry Pool area. You will find the Fairy floating above the water, but thankfully the Deku Link can hop across the stream to capture the Fairy. If you wait until nightfall, you'll find the Stray Fairy floating around East Clock Town, and you can use a nearby Flower Pad to grab it.
With the lost Fairy in hand, return to the Great Fairy shrine to receive the ability to shoot bubbles - something that will be very useful to you at this point in the game. When you exit out of the Fairy Shrine, you will find a small boy (Jim) who is trying to pop a balloon with a very familiar face on it. If you use your Deku bubble attack to pop the balloon, Jim will allow you to play a game that will give you access to the secret passageway that will lead you to the observatory. Jim will call four friends, the five will then go hide and you will need to find them. The first two are in North Clock Town where you are, and they usually like to hide in the corners. Numbers three and four are located in East Clock Town. One will jump off a roof with a chicken, and the other is located on the roof of the inn, and you will need to use the flower to launch yourself up and scare him off. The final boy is in West Clock town, near the top of the area.
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With all five found, you will be given a passcode (be sure to write it down, as it is random) that will give you access to the secret passage in East Clock Town.
Speak to the boy in East Clock Town, and give him the passcode that Jim and friends did to access the passageway to the Observatory.
Once inside, you will need to hop from platform to platform over the water. Against the far wall, a Spider will drop down. You may recognize these from Ocarina of Time, and they are defeated the same way here. When its back is turned to you, fire off a bubble to kill it. Then make your way around the corner into a large room with another balloon (which just so happens to be blocking a ladder).
Pop the balloon with another bubble and climb the ladder to access a new room with a familiar character inside. If you played Ocarina of Time, you will recognize the Scarecrow. Just as in the previous game, you can teach him a song, so be sure to make it one that you can easily remember!
Climb the brightly colored stairs to arrive at the telescope. Speak with the old man, and then look through the telescope when you have the chance. Turn the viewfinder until you see the Clock Tower, and zoom in to find Skull Kid on top of it, then a blue object will shoot to the ground outside. Exit out of the telescope mode, and go out the small door to find the Moon Tear.
Go back to the center of town to the flower launcher to trade the Moon Tear to the Deku for a Land Title Deed. After the trade, the Deku will fly away and you will be able to use the Flower Launcher to shoot yourself into the air and glide over to the clocktower to find a Heart Piece.
Now that you have the Land Deed, it is time to get another Piece of Heart. Wait until after midnight on any night, and use the launcher to get on the roof of the inn. Go inside and run down to the bottom floor. You will find a hand coming out of the toilet asking for a paper. Give him the land deed to receive a Heart Piece.
Since you can't really do anything else to advance the plot until the night of the third day, you may want to run around the town and explore a little bit. In North Clock Town, you can find Tingle who is being held up by a balloon. Pop the balloon and he will sell you a map of Clock Town for five rupees.
To progress the story further, wait until after midnight on the final day and you will see a cut-scene of the clocktower opening. Use the flower launcher to get to the opening and run inside to confront Skull Kid. You will only have five minutes to save the world, so shoot Skull Kid with a bubble to knock the Ocarina out of his hands. When Link picks it up, he will have a flashback of Princess Zelda teaching him the song of time. Since you cannot defeat the masked menace yet, play the Song of Time to return to the first day. Tip: You can play the Song of Time backwards to slow down time.
When you arrive back in the first day, go inside the lower entrance to the clock to encounter the Mask Merchant. He will see that you have the Ocarina and will teach you the Song of Healing, which will transform you back into Link. He will then tell you the story of Majora's Mask.
Even though you can now leave the town as normal Link, there are still a couple things to do here.
You also have the Notebook, which is an extremely useful item to keep track of what quests you have completed, as well as ones you have not yet completed.
Whenever you complete an important event or meet someone important, it will be recorded in this book. If you check it out, you will see that the passcode has been recorded in it, so you don't need to keep it written down if you ever need to go back into that tunnel. The book will also give you the time of day, which is pretty helpful.
Before you head off into the wild world of Termina, there's a lot more to do on the side After The First Three Days.