The Buddy System
The story begins late at night as Mario and Luigi attempt to stop loud booming noises coming from the Transport Tubes in Princess Toadstool's basement. Mario finds the pipes to be cluttered with trash, discovering on a sneaker that it all belongs to Bowser. He hops into the pipe (leaving Luigi behind and taking the sneaker with him) to search for the tyrant.
Soon, Mario finds Bowser (still wearing the other sneaker) instructing Lemmy on dropping bombs at a wall's base and running away. Foolish Lemmy repeatedly asks him to go over it again and again, and finally Bowser questions if he knows where the main pipe really is. Lemmy tells him that Mouser told him where it was, and that blowing it up would cause the entire underground area of the Mushroom Kingdom to flood; this would make transportation impossible. Unfortunately, Bowser reveals that Lemmy already blew up ten sections, leaving one Warp Pipe remaining. Lemmy uses four bombs to make sure it works, but the results are catastrophic: Luigi hears the explosion from the basement; Lemmy is blasted out of the underground world; and Mario and Bowser are sent flying towards a colony of Mice.
The Mice chain Mario and Bowser together, and Bowser ends up blabbing his plans to flood the underground world (after the Mice accuse Mario of being the smarter of the two). The lead Mouse questions why he planned on doing this, and Bowser explained that he would open a taxi service that people would use in place of the useless, flooded underground chamber. The Mice tell them that their location was very incorrect, and show them the real water main. In fact, the Mice light the fuses of several bombs and demonstrate how they would blow up the main; thus flooding the underground.
Bowser drags Mario to a Transport Tube, running as quickly as he can. However, the tube does not take them anywhere, because, as Mario explains, the pipes de-activate after the water in the underground reaches a certain level. Mario and Bowser have to work together to get the valve of the water main turned in order to stop the water (as they do, Bowser is wearing a plumber's hat like Mario's). After it stops, an emergency drainage system activates, and the Transport Tubes begin working again. As the two leave, Bowser grabs a large branch off of a broken tree.
The instant the two reach above ground, Mario fights Bowser with a plunger as he counters with his branch; but Lemmy soon arrives with another bomb - and drops it. The bomb narrowly misses Mario and Bowser, breaking their chain instead. As Bowser chases Lemmy (now wearing both of Bowser's sneakers) through the kingdom, Mario returns to the castle to find that everyone else is celebrating because they think Luigi fixed the plumbing (though it was really Mario and Bowser who stopped the booming noises). Princess Toadstool tells Mario that it appears his brother is a better plumber, and a reluctant Mario agrees.