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The game starts out with Link riding on Epona when a mysterious Skull Kid appears along with two fairies, Tatl and Tael. He knocks Link off Epona and takes his Ocarina, then he steals Epona.
Chase the Skull Kid
You now have full control of Link. Spend some time adjusting to the controls and practice your sword swings on the bushes if you want. When you're ready, head through the tunnel to enter into the next area. Jump from stump to stump and enter into the next tunnel.
When you enter this tunnel, Link will fall down and land on a flower. The Skull Kid then appears and proudly announces that he has gotten rid of your horse before using his magic to transform you into a Deku Scrub. As the Skull Kid runs off, Link attempts to chase after him but finds himself blocked by Tatl. However, in doing so, the Skull Kid and Tael accidentally leave Tatl behind, leaving her with Link. Head through the door and down the tunnel, and Tatl will force you to bring her with you.
In front of you should be another flower. This is, in fact, a Deku Flower, and as a Deku you can use them to fly for a brief period of time. To do so, stand on the flower and hold down 
. After a puff of smoke rises from the flower bud, release to launch into the air. Use the control stick to maneuver Link and to put the flowers away and drop to the ground. If Link starts to kick his legs and the flowers start to spin more slowly, then that indicates that Link can't fly for much longer and is going to fall, so don't spend too much time playing around in the air.
Use your new powers to fly to the other side of the room and head though the door. In this room, you must fly from tree stump to tree stump. There is a treasure chest on a stump in the direction of where you entered the room, so fly to it and open the chest to receive ten Deku NutsFile:OoT Item DekuNut.png. Deku Nuts can be used to stun enemies and can be equipped to an item slot. You can also use them during flight: press 
while flying to drop a Deku Nut and stun enemies below.
There should be a tree stump with a tunnel on it in the room you are in. Use the Deku Flowers to fly to it and check out the small tree in front of the tunnel, if you wish. Then head into the tunnel. You'll go down a twisted hallway which will straighten itself out and lead into a cellar-like area. The door behind you will shut itself. Now go up the nearby ramp and then up the steps. You'll see the Happy Mask Salesman, who will tell you that you will be stuck in your current form unless you can retrieve your Ocarina. He will also tell you to fetch the mask that the Skull Kid took from him before three days pass.
Welcome to Clock Town
Upon leaving the Clock Tower, you will find yourself in Clock Town. Clock Town is divided into five sections: North Clock Town, South Clock Town, East Clock Town, West Clock Town, and the Laundry Pool. You are currently in South Clock Town, which is basically the central area of town. Tatl suggests that you seek out the Great Fairy for assistance in this matter. The Great Fairy is located in North Clock Town, so loop around the Clock Tower and head north.
Help the Great Fairy
When you enter North Clock Town, head left and up the path into the Great Fairy Fountain. Sadly, it seems that the Skull Kid split the Great Fairy into several smaller Stray Fairies. In order to get the Great Fairy's help, you must find the missing Stray Fairy and bring it back to the fountain.
The Stray Fairy can be found in two locations, depending on the time of day:
- During the day the Stray Fairy can be found in the Laundry Pool. Head to South Clock Town and go up the ramp in the southwestern corner of the area to enter the Laundry Pool. Skip across the water to grab it.
- At night the Stray Fairy moves to East Clock Town. It can be found hovering around the Treasure Chest Shop (the large building shaped like a treasure chest) and you need to use the nearby Deku Flower to get it.
Once you have the Stray Fairy, return to the Great Fairy Fountain to reunite it with the others. The Stray Fairies come together to form the Great Fairy of Clock Town, who will reward Link with the ability to use magic. With magic at his disposal, Link can shoot snot bubbles from his snout by pressing . The longer you hold the button, the bigger the bubble will be, but if you hold it too long the bubble will pop. The bubbles can be used as little mini projectiles; though they are otherwise worthless in most situations, they are the best you can do for now.
Befriend the Bombers
Nearby the Fairy Fountain there is a young boy in a red bandana shooting at a balloon of the mask worn by the Skull Kid. Pop the balloon using your bubble shooting technique and speak with the kid. He is the leader of the Bombers, a Clock Town's resident street gang composed of little kids. The'll offer you a chance to take the initiation test, which consists of a game of "hide and go seek". Accept the offer.
The goal here is to find all five of the bombers before the morning of the next day. To catch a Bomber, run up to him and tag him. The Bombers scurry around very quickly when found, so use your dash attack or, if you feel like wasting some ammo, use your Deku Nuts. The Bombers can be found in the following locations:
- North Clock Town: Playing near a tree in the southwest corner of the map.
- North Clock Town: Hiding near the playground in the northeast corner of the map.
- West Clock Town: Walking in plain sight in the main plaza.
- East Clock Town: Standing on the balcony of the Stock Pot Inn (located near the Treasure Chest Shop, where the Stray Fairy appears at night). Head into the Inn when it is open and go through the door in front of the staircase on the second floor, or just use the Deku Flower.
- East Clock Town: Head up the path on the right side of the Milk Bar (located on the eastern edge of town) and chase him off the ledge and into the plaza.
When all five Bombers have been captured, they will inform you that only humans can be members of the Bomber's Gang. However, because they like you, they will tell you the secret code to their secret base. The code is randomly generated. Be sure to write it down for later use. If you forget the code, speak with any of the Bombers with the blue bandanas to have them repeat it. With the code in hand, head into East Clock Town and speak with the yellow bandana-wearing Bomber in the northeast corner of town. Input the code and he will give you access to the path that leads to the Astral Observatory.
The Path to the Observatory
The path to the Astral Observatory is fairly straightforward. Simply head through the sewer. There is a Skulltula on the way there that can easily be defeated with a couple of snot bubbles when they turn around and expose their backsides. You will eventually reach a room with a balloon blocking your path. Use your bubbles to break it and climb the ladder into the observatory.
Obtain the Moon's Tear
In the observatory you can speak with Pierre the Scarecrow if you wish to speed up time, otherwise head up into the main room of the observatory and speak with the old man there. When he asks if you would like to look through the telescope, agree.
The telescope can be used to observe the area surrounding the observatory, which is on the eastern edge of Termina Field. Move the telescope with the Control Stick and press to zoom in and to exit. Move the telescope up to the top of the Clock Tower and zoom in on the Skull Kid. When he looks up at the moon, which is extremely close to Earth and has a face, something will fall from the "eye" of the moon and it will land in front of the observatory. Exit from the telescope and go outside using the nearby door. Pick up the object that fell. This is a Moon's Tear, and it will help you confront the Skull Kid at the top of the Clock Tower. Leave the observatory back through the sewer and head back to Clock Town now.
Trade the Moon's Tear
Return to South Clock Town and head for the yellow Deku Flower. If you never approached the Deku Flower before, an Business Scrub will fly down and occupy the flower, informing you that this is his land. Equip the Moon's Tear in an item slot and show it to the Business Scrub by using it as an item. The Business Scrub will be so mesmerized by the Moon's Tear that he will give you the Land Title Deed, which gives you free access to this flower for your own personal use. You can now use this flower to fly to the entrance of the Clock Tower, however, the door will not open until midnight on the third day. If you went through all the story events one after the other, then you will likely have a lot of time to kill.
On the third day, be sure to use the Deku Flower to climb to the top of the scaffolding in the middle of the area to find a chest that contains 50 rupees.
Confront the Skull Kid
On midnight of the third day, the entrance to the Clock Tower will open. head up the stairs and you will find yourself on top of the tower, with the Skull Kid and the Moon overhead. You cannot harm the Skull Kid in any way, but what you can do is send a snot bubble his way to knock the Ocarina of TimeFile:OoT Item OcarinaofTime.png out of his hands. Once the Ocarina is in your possession, there will be a quick flashback where you will remember Zelda playing you the Song of Time:
Take out your ocarina (which has somehow transformed into a set of brass pipes) and play the Song of Time. When asked if you want to return to the Dawn of the First Day, choose "Yes". The game will save and you will be sent back in time to the first day.
The Song of Healing and the Deku Mask
Head inside the Clock Tower's base and speak with the Happy Mask Salesman. He will be so overjoyed that you found your Ocarina that he will teach you the key to breaking your curse, the Song of Healing:
After playing the Song of Healing, the curse will be lifted and you will receive the Deku Mask which, when worn, will allow you to assume your Deku form once again. In return, the Happy Mask Salesman asks for the mask Link promised he would get. The Salesman promptly flips out upon realizing that you don't have the mask. He demands that you find the mask before something terrible happens. Looks like you have no choice!
Upon leaving the tower base, Tatl will recall Tael's words on the Clock Tower. Tatl comes to the conclusion that the locations Tael was referring to correspond to locations here in Termina. She suggests that you head south to see what's what.