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On a quest to find a friend he lost during his last adventure, Link finds himself deep in the Lost Woods. Suddenly, two fairies appear, frightening Link's trusted mount, Epona, and causing her to knock him off, rendering him unconscious. The mysterious Skull Kid appears, and after playing around with Link's ocarina, Link awakens, only for the Skull Kid to escape on Epona. Chasing after him, Link falls into a hollow tree and awakens in a cavernous complex, where the Skull Kid turns Link into a Deku Scrub, leaving him in the caves. With the help of Tatl, one of the fairy friends of the Skull Kid who became stranded with Link, the transformed hero makes his way out of the caverns. Here, he encounters the Happy Mask Salesman, who agrees to return him to his original form, if he can manage to get back his stolen ocarina. In return, the Salesman asks Link to retrieve Majora's Mask from the Skull Kid, who had stolen it prior to the events of the game.
Link investigates Clock Town, the central city of the land of Termina in which he now finds himself. In town, Link comes across a Stray Fairy, which he returns to the Great Fairy Fountain in North Clock Town. As thanks for returning her to her original shape, the Great Fairy of Magic grants Link the ability to blow bubbles, at the cost of magic. Using the bubbles, Link pops a balloon in North Clock Town, impressing Jim, leader of the Bombers Secret Society of Justice, who had unsuccessfully been trying to pop the balloon. Link plays Hide-and-Seek with the Bombers, and while he is not allowed to become a member, he is granted access to their hideout that leads to the Astral Observatory. Gazing at the Moon through Shikashi's telescope, Link spots a Moon's Tear falling from it and landing outside. Link trades this to a Business Scrub in South Clock Town for the deed to his Deku Flower, which Link uses to gain access to the Clock Tower on the eve of the Carnival of Time.
He confronts the Skull Kid on top of the Clock Tower, who attempts to use the power of the mask to cause the Moon to destroy all of Termina. Link fails to find a way to stop the Skull Kid, but manages to knock the Ocarina of Time out of his hand. Upon touching the Ocarina, Link remembers the "Song of Time", taught to him by Princess Zelda before he left on his adventure. In his Deku form, the Ocarina of Time takes the form of Deku Pipes; Link plays the "Song of Time", resetting the cycle of time to the first of the three days that occur before the Moon destroys Termina. Link returns to the Happy Mask Salesman, who teaches him the "Song of Healing", a powerful song that heals people's sorrows, turning them into masks. The curse is drawn out of Link, creating the Deku Mask, which allows him to transform into a Deku Scrub and back again at will.
Deku Link has a multitude of powers, the most basic of which is a brief mobile Spin Attack, which provides a boost in speed and has the ability to quickly defeat weaker enemies, stun many larger enemies, and cut grass. Additionally, Deku Link can shoot bubbles at the expense of some of his Magic Meter. The range of these bubbles increases the longer Link charges them before firing. They are somewhat inaccurate however, and will stun or bounce off extremely armored enemies rather than dealing damage. Deku Link can also use Deku Flowers, burrowing into them to hide and to launch himself into the air, damaging enemies in his path and allowing himself to fly within a certain radius using helicopter-like flowers. Deku Link's flowers and flight ability can also be activated by updrafts. While using this ability, Deku Nuts can be dropped with the B button, hitting unwary targets situated directly below Link. While on the ground, Deku Link can use Deku Nuts to stun enemies the same way Hylian Link can. Deku Link can also generate a full body shield, but it is wooden and cannot prevent fire effects, and he cannot move while it is up. Deku Link, as well as his statue created by the "Elegy of Emptiness", are too light to depress most switches, making his statue largely useless.
When Deku Link encounters water, he can hop across the surface to reach the next area. He can hop five times, each higher than the last, but will sink if he lands on the water after the fifth hop, causing him to reappear on the last point of stable land he stood on. To make this move more effective, a spin attack can be initiated before Link reaches the water; the speed increase from the spin attack will be applied as long as Link is hopping, greatly increasing the distance he can travel over the water. When Link uses his Ocarina of Time, it transforms into the Pipes of Awakening. Deku Link is made of wood, so he is extremely vulnerable to fire; contact with it (even with his shield up) causes the screen to fade to black, and Link will be reset to the entrance of the room in a similar fashion to when he falls into a bottomless pit. Since only Deku Scrubs are allowed to enter Deku Palace, Link must use this mask to gain access to it. Once inside the Palace proper, however, Link is free to remove the mask; but if spotted by a Deku Scrub, he is thrown out.
Just as Link's Goron and Zora forms each transform him into the shape of a recently deceased being, many believe that Link's Deku form is that of an existing being. It is heavily hinted at that the mask holds the spirit of the Deku Butler's Son. Early on in the game, Link discovers a dead tree that resembles his new Deku form. Tatl comments on this, noting the sadness in its face.
This is not elaborated upon until after the completion of the Woodfall Temple. After Link manages to keep up with the Deku Butler throughout the maze-like Deku Shrine, the butler presents Link with the Mask of Scents, once owned by his lost son. He also mentions how Link reminds him of his son. During the game's ending, the Deku Butler is seen kneeling in front of the withered tree, implying that it is the remains of his long lost son. Additionally, when the "Elegy of Emptiness" is played, a shell of Link's current form is created. Link's Goron and Zora forms shed statues which look like the individuals the two masks were created from, rather than appearing as Link does when he wears the masks. In this vein, the Deku Mask's statue is similar in appearance to the withered tree, and decidedly different from Link's Deku form.
Deku Link is featured as a sticker. His sticker grants +31 resistance to electric attacks, and can be applied to anyone.