Team up with Bowser Jr. in a free-roaming 3D adventure to stop his dad’s rampage. Run and jump across a series of islands to collect the mysterious Cat Shines, and battle against the colossal Fury Bowser whenever he emerges from the water to wreak havoc.

During a bright and clear day, Mario walks down a path in front of Peach's Castle, near the same location where he found the broken Clear Pipe at the beginning of the main campaign. He notices small puddles of black goop on the path and follows them, eventually stopping at a mass of black graffiti shaped like Shadow Mario's logo from Super Mario Sunshine. The graffiti expands to create a portal that Mario falls through, transporting him to Lake Lapcat, where a rainstorm is occurring.

Shortly after Mario lands, he encounters Bowser, who has become a larger and more powerful form known as Fury Bowser. Mario finds a Cat Shine in the surrounding area, which clears the goop off of a nearby lighthouse. Fury Bowser is blinded by the beam of light that shines from the lighthouse, and retreats into the Fury Sun in the middle of Lake Lapcat. Immediately afterward, several islands emerge from the water.

After Fury Bowser retreats, the storm clears and Mario finds a panicking Bowser Jr., who explains why Bowser transformed. He shows Mario a picture he painted of his father and paints it black with his Magic Paintbrush, showing that Bowser Jr. was the one who corrupted Bowser. He realizes that both he and his father are in trouble, reluctantly asking Mario to help him, but clarifying this would not happen under normal circumstances. Mario agrees to do so, with Bowser Jr. joining him for the rest of the adventure.