In chapter 2 of volume 2, Bowser is angry at the failures of his minions, so he activates the Mekakuppa, knowing Mario and his friends are headed to Vanilla Dome. The trio is attacked by the robot, which tries to stomp with its feet, then crushes them with metal nasal mucus. Mario tries to fight back using Yoshi as a bat, but ends up angering the Mekakuppa, which pulls out a giant drill from its wrist. While trying to hit Mario, the Mekakuppa creates a hole in the Vanilla Dome, creating a connection with Vanilla Dome 3's lake. From that, the Dolphins fall into the lake and take Mario, Luigi, and Yoshi to the surface, where Mario plugs the hole, trapping the robot. However, the Mekakuppa resurfaces and knocks out the trio. Mario flies away with a P Balloon and finds a 3-Up Moon in the sky and becomes Moon Mario. While being unfazed by the robot's laser, Mario grabs a Cape Feather in the Item Storage, then tickles the Mekakuppa's nose, making him sneeze out all of his mechanical components. Mario then rebuilds the robot into a Ferris wheel.
In the first part of chapter 11 of volume 4, while traversing the Bowser's Castle hall full of Bowser Statues, a giant Bowser Statue emerges from the lava. Mario tries to destroy it with a punch, but realizes it is not made of stone, but metal, discovering it is the Mekakuppa, rebuilt and painted. Mario, however, gets the upper hand and, being badly rebuilt, the Mekakuppa explodes after a well-placed hit from Mario.