The story starts off in the Mushroom Kingdom, during the yearly Sticker Fest. An event much similar to the Renaissance Festival, except instead of artisans, people craft stickers which contain magical powers that come from the 3-D world around them. Bowser, angry that he was not invited to the event, thinks it would be fun to play a prank on everyone during the festivities. But something goes wrong during Bowser's joke and Six Royal Stickers ended up becoming attached to Bowser and his minions, giving them new powers. It's up to Mario and a Sticker faerie named Kersti too set off and get the stickers and bring them back to the Mushroom Kingdom.
Mario will travel to many new places, particularly new areas that deal with nature, such as snowy mountains and fiery volcanoes. As he retrieves the stickers he will gain new powers that he can use in combat and also to help him solve puzzles in the world around him. Eventually in the game Mario will even be able to create his own unique blend of stickers that can give players the certain edge they need.