Majora's Mask starts by showing Link wandering through the Lost Woods on Epona, his horse, when he is attacked by two fairies and an imp wearing a strange mask. It is said that Link was looking for an old friend. After Link defeated Ganondorf in Ocarina of Time, Princess Zelda sent Link back in time seven years, so he could relieve the part of his life he spent resting in the Temple of Time. And so Link went on a personal journey trying to find a long lost friend he lost when was sent back in time. Many say that that friend was Navi, his fairy, but it has never been proved.

The fairies scared Epona, who jumped up and knocked Link off its back, and Link blacked out. When Link woke up, a kid wearing a skull-shaped mask was going through his things. The kid, the Skull Kid, took his magical ocarina, and when he saw that Link had awoken, he hopped on Link's horse, Epona, and ran off. But Link was too quick for him and he also grabbed onto the horse as the Skull Kid was riding away. Link was knocked off the horse, but continued to pursue his horse and the Skull Kid. As he chased the chased the Skull Kid, the Skull Kid went through a stone barrier, and left one of his two fairies behind. The fairy's name was Tatl. Tatl was locked on the outside of the stone barrier, and so she had to help Link get back in so she could get back together with the Skull Kid. Link then stumbled across a portal to a parallel world and met with the Skull Kid on the other side. The Skull Kid then turned Link into a Deku Scrub with the dark magic powers that Majora's Mask had given him.

Link found himself inside a giant clock tower in the center of Clock Town. There he met the Happy Mask Salesman from Hyrule Marketplace. He owned the Happy Mask Shop from which Link traded masks in Ocarina of Time. The Happy Mask Salesman told Link that he could change him back to normal if Link could retrieve the item that was stolen from him by the Skull Kid. Majora's Mask. But he told Link that he was a very busy man and he had to leave in three days.

Link walked out of the clock tower, and into a world where everything revolves around time. The townsfolk even had a special festival to honor time. It was the Carnival of Time, which occurs once a year. Link has three days until the festival arrives. But the moon is getting closer by the minute, and Link only has 72 hours.

Link, stuck inside the body of a Deku Scrub, must wait until the Carnival of Time to reach the top of the Clock Tower to face off with the Skull Kid to get back his Ocarina of Time. He completes certain tasks allowing him to reach the tower. When the clock struck midnight on the third day, the doors to the top of the Clock Tower opened and allowed Link to enter. Link found the Skull Kid on top of the Clock Tower, with his precious ocarina.