Sometime after the events of the previous game, Mario and his friends are enjoying a relaxing day on Princess Peach's Castle grounds, before a Spark abruptly falls from the sky. It turns out that he was fleeing from a gigantic manta ray, which proceeds to spread Darkmess, a type of dark matter, across the land and kidnaps Rabbid Peach. Mario and Beep-0 leap in to save her, before the two manage to hold off waves of enemies. Soon enough, an entity named Cursa arrives to confront them, but the heroes are rescued by their friends in their new ship, the WM ARC, where they are introduced to the onboard AI, JEANIE. JEANIE explains Cursa's plot to corrupt the whole galaxy with its Darkmess, as well as the existence of the Sparks, and the heroes set out on their interstellar journey.
