Arriving in Links Universe to the sudden location of the kingdom's Greenleaf, Fontaine, Ignis, Terrera and Illusio. Upon arrival, they spot a young looking Link running through the forest on horseback as he chased after a young imp wearing a curious mask. Splitting up to go after him, they learn the identiy of the Imp, the Skull Kid, who has been wearing the dark mask embedded with the might of a dark entity. He strips Epona from link and curses him with a Deku mask, turning him into a Deku Scrub. But as Skull Kid leaves, he leaves behind one of his fairy friends, a small female fairy named Tatl. Using Links new Deku abilities, they travel to the linked town of Termina and meet the H.M.S, who helps link by absorbing his Deku Scrub form into a mask. He soon explains that the mask the skull kid wears is called Majora’s Mask, a powerful artifact used by an ancient tribe for their hexing rituals. The Skull Kid has stolen it and is now using its dark magicks to cause mischief and chaos. It was even threatening Termina’s destruction by calling down the moon to crush everything.

Link plays the song of time after Usopp puts the Skull Kid to sleep, rewinding time. To Taels directions, they head in 4 directions to a Swamp, Mountain, Ocean and Canyon, and bring the 4 guardians to termina. But not before help comes from Maka and Soul as well as a young boy named Crona, who join without hesitation and to ask a few questions for the Skull Kid.

Over the course of the days, they visit the Deku, Goron and Zora races and  battle against the kingdoms occupying those areas as well as a few robots. They even come to acquire Black Star and Tsubaki from the goron kingdom, and rescue Death the Kid along with the Thompson Sisters from the Gerudo Pirates. Even discovering something new, a blue robot that was captured to sell, which identifies itself as MegaMan. At the Canyon area after beating Terrera and Illusio, they meet a creation of Aelita's mother called Serenade, a medical robot who was for mysterious purposes.

Finally recruiting all four guardians, they were now ready for Skull Kids onslaught to bring the moon down. After playing the song, they call all four guardians as they come and stop the moon for good. But as Tatl and Tael reunite, something very surprising happens even the heroes could not have predicted. The mask itself….was alive. It was introduced as Majora’s actual spirit that has long since slept within the mask before the Skull Kid donned it. He also claimed he would destroy this world. He flew into the moons mouth as the moon spoke about consuming it all and started moving once more, making it hard for the guardians to keep from crashing down. The only way to stop all of it was to confront Majora head on. So, our heroes enter the moon and come across a small child with the supposed mask. After giving one to Link, the battle begins. Inside of a chamber, the mask springs to life and brings with it its allies, the masks of the fallen beasts. They then move in to attack the group head on. Battling them, its dancer form and its wrath form, Link uses the mask to become Fierce Deity Link and defeat Majora, ending the demon’s reign for good. The moon vanishes as the mask becomes an ordinary mask that the H.M.S collects and goes on his merry way. After witch, Maka and the meisters become the final ones needed to join the team as part of the supposed prophecy. But while this happened, Flux and Ian were going down a list of missing robots, foreshadowing something to happen in the distant future. It was then revealed that Flux’s plans were close to completion.