Majora's Mask is first introduced after the Happy Mask Salesman removes the curse that was placed on Link by Skull Kid. The Salesman explains that the Mask is an ancient artifact that was used by an ancient tribe for its bewitching rituals, but the Mask's wicked power became so great that it was sealed away to prevent a great catastrophe. However, since the ancient tribe vanished, no one accurately knows the true nature of its power. The salesman fears the great devastation that could befall Termina if the Mask is not taken back from the Skull Kid.

When the Skull Kid donned the Mask, it created Termina out of a combination of the evil within the Mask and the Skull Kid's memories and delusions.

For a majority of the game, the Mask is worn by Skull Kid on the Clock Tower, drawing the Moon to Termina. Although the Skull Kid is unaware, Majora's Mask is gradually beginning to take complete control of his mind, with his once harmless pranks becoming malicious acts of evil. Prior to the game's events, Skull Kid used the power of the Mask to prank and curse others around him, such as Kafei.

After the Four Giants are called, the Mask abandons Skull Kid and enters the Moon so that it can push it through the Giants' blockade and complete its destructive path. Link then proceeds to follow Majora's Mask into the Moon. Once inside, he finds four childrenwearing the Boss Remains and one lonely child under a Tree wearing Majora's Mask. If Link gives all his non-transformation masks to the four children, the child wearing Majora's Mask will give him the Fierce Deity's Mask. He will then take Link to the final boss room.

After the young hero and Tatl defeat Majora's Mask, they return to the land of Termina where the Happy Mask Salesman informs them that the evil inside the Mask has disappeared.The Mask is last seen as the Happy Mask Salesman departs with it in his hands.