Suddenly, while riding in the forest, Link and his horse Epona ran across something rather strange. Two fairies startled Epona and Link fell to the ground, passing out. An outcast called Skull Kid, friend of the fairies, mugged Link and stole his ocarina. He then mounted Epona. Link woke up just as they began to ride away. Link quickly followed them into a tree, where he fell into a strange portal.

Link ended up in a cave on the other end of the portal, where he once again encountered Skull Kid and the fairies. Skull Kid casted a spell upon Link, and he became a Deku Scrub! Skull Kid fled, but one of the fairies fell behind. Her name was Tatl. She teamed up with Link, but said it was only temporary until they found a way out of the cave. They eventually found themselves in a place with many gears, almost like a clock. It was there that Link ran into a familiar face: the Happy Mask salesman, from the Hyrule Market! Apparently, he had been following Link because Skull Kid had stolen something very important from him as well: Majora's Mask. The mask was the work of an ancient cult, and was filled with pure evil. With Skull Kid having such a weak will, it took him over easily. Because of this, Majora's Mask had caused Skull Kid to call the moon to fall towards the surface, which would, of course, destroy everything. With only 72 hours left, Link had to recover the mask, and the salesman would then return Link to his normal Hylian self.

The place truly was a clock; upon exiting from a door, Link found himself in Clock Town, where a grand clock stood in the center. The salesman had not lied: the moon hovered over the planet with an evil gaze. This strange new land was called Termina, and it had many parallels with Hyrule. Link found many of the same people in Termina that were in Hyrule, but some of them had very different personalities from their Hyrulian counterparts.

At the very end of the third day, as the moon was about to crash, the Deku Scrub Link found a way to the top of the clock tower, where the mask-wearing Skull Kid was. Majora's Mask had made Skull Kid powerful, and there was no way Link could defeat him. Link was, however, able to recover the Ocarina of Time. Recalling the Song of Time from his adventures in Hyrule, Link played it, hoping something might happen. Interestingly, playing the Song of Time in Termina returned Link to the exact point where first he entered Clock Town, at the very same time! He yet again, had three days to find the mask!

He went to the salesman, who taught Link the Song of Healing, which restored him to his normal self. This also produced a mask, which Link could use at any time to become a Deku Scrub. When the salesman discovered that Link had actually not recovered the mask, he became enraged, but soon got over it, and trusted Link to complete the quest. By traveling back to the first day, Link was able to continuously re-live the same set of three days, carrying with him all of his important items.

He set off to help all of the people who had been troubled by Skull Kid's mischief, and soon found out some things about four ancient guardians of Termina, who had apparently been Skull Kid's friend centuries ago. If they could all be found, they could stop the threat of the moon.

Link traveled through several temples, made the use of many masks, and found all four of the guardians. When he called them to Clock Town by their song, Oath to Order, they held up the moon. Link then went inside the moon and destroyed the evil within Majora's Mask.