The hero and their team track down the Darker Lord through the lands of Powdered Peaks, Peculia and Nimbus, before reaching the Darker Lord's Domain in The Sky Scraper, fighting previous bosses along the way.

Enraged, the Dark Curse tries to possess the player's Mii, until the Great Sage intervenes and becomes possessed instead, becoming the Darker Lord. The team fights the Dark Lord, and upon defeating them, the heroes discover that the Dark Lord was a common Mii possessed by a small blue wisp known as the Dark Curse. The hero is tasked with saving all of their friends, with some help from the Great Sage. Upon arrival, the Dark Lord attacks again, stealing the new companions, but failing to steal the hero's powers. After retrieving their faces, the Fab Fairies open the door to Karkaton, and the team head out. Before they can open the door, the Fab Fairies have there faces stolen by the Dark Lord. The hero is tasked with saving the three Fab Fairies of the Realm, who provide the team the way to the Dark Lord's castle in Karkaton.

The team continues to the Realm of the Fey, where the Dark Lord attacks again, stealing the hero's companions and their character class again, prompting the guardian to provide a new group of character classes. After the guardian provides the hero with new powers, they head out through Neksdor, meeting three new companions and the Genie of the Lamp. Afterwards, the team enters the kingdom of Neksdor, only to be attacked by the Dark Lord, who steals the protagonist's companions and renders the protagonist without a class. Along their journey, the player creates more companions, meets the Great Sage, and reaches Greenhorne castle, continuing the quest after the Dark Lord steals the faces of the King and the Princess.

The protagonist chooses a character class and is sent on a journey to stop the Dark Lord. The game begins with the main protagonist, a Mii of the player's choice, arriving in Greenhorne Town, which is soon attacked by the main antagonist, the Dark Lord, who wields the ability to steal faces from Miis and use them to control peaceful creatures, turning the creatures into monsters. The Nintendo Switch remaster also introduces a new makeup and wig feature which allows players to further customize their in-game characters, including options not available on the console's Mii Maker application, as well as a horse that can help in combat.

Miitopia supports the ability to import Miis and their trait settings from Tomodachi Life, as well as from a player's friend list. The game also supports Nintendo's line of Amiibo figures, which allow players to use unique cosmetics on their Miis. Similar to Tomodachi Life, Miis and their relationships out of combat with each other affect the game, such as Miis not getting along with one another making combat more difficult. Playable characters are created with Mii avatars, with them having certain personality traits that influence their role in combat. Miitopia is a role-playing video game with life simulation elements, starting with standard character classes or 'jobs' such as warriors and mages, but as the game progresses, more classes appear. Players' stats and actions can be accessed from the 3DS's bottom screen. Two Mii characters engaging in the game's combat sequence on the 3DS version.

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