The game takes place after Mario and Luigi: Bowser's Inside Story. Fawful sits down in a forest in the Bean Bean Kingdom. He plans to make a species that can destroy Mario, Luigi and Bowser. He flies to Bowser's Castle and goes into the freezer room and sees 15 frozen shroobs. He laughs an evil laugh while pulling down a lever to thaw out the shroobs. The screen fades to Mario and Luigi's house. Stuffwell was sitting against a wall. Mario bought a new HD TV to put on a wall. Luigi had the Poltergust 3000 by his bed and the F.L.U.D.D. by Mario's bed. Mario and Luigi were sitting in their chairs by their new fireplace. Toadsworth runs in the house. "Th... th... the shroobs are bb... back!" Toadsworth screams. He faints. Mario and Luigi jump out of their chairs and run to Peach's Castle.