Mario, Luigi, Princess Toadstool and Toad have ventured to Robo Land in pursuit of King Koopa, whom they had intended to stop. However, after finding King Koopa, Mario and his friends soon find themselves running for their lives, as Bullet Bills are being fired in their direction continuously. After hiding behind a building, Luigi and Princess Toadstool ponder as to why a metal monster is attacking them in the first place. Looking around the corner, they see that the monster is actually King Koopa wearing a Robo Suit. Now calling himself "Robo Koopa", King Koopa demonstrates the power of his suit by shattering a building with a single punch. Robo Koopa threatens to destroy Mario's group, but as he fiddles with the buttons on the chest of his suit, Mario and his friends make a run for it. Robo Koopa continues to chase Mario's group through Robo Land, and fires more Bullet Bulls in their direction, which they dodge by ducking.
Just as Robo Koopa threatens to blast Mario's group with his "Super Toes" (cannons in his feet), a strange, feminine voice speaks, as a robotic arm extends up through a hole in the ground and pushes several buttons on the robo suit. The voice states that her actions should mess up Robo Koopa's controls for a while. Robo Koopa starts walking backwards uncontrollably, and aimlessly fires a Bomb Plant, which blows up another building. Robo Koopa announces that he'll return, and is helpless as his robo suit takes him elsewhere.
With Robo Koopa gone, the robot who had stopped him climbs out of the hole, greets Princess Toadstool, and introduces herself as Bunsen to Mario, Luigi and Toad. Bunsen insists that they leave before Robo Koopa fixes his robo suit, and pulls Luigi down the hole with her, prompting the others to follow suit. While sliding down the hole, Princess Toadstool and Bunsen have a brief discussion about how King Koopa tricked the genius inventor Dr. Nerdnick into building him a robo suit. At the bottom of the slide, the group proceeds to climb up another shaft, and conclude that Dr. Nerdnick may be the only person who knows how to stop Robo Koopa.
Upon reaching the top of the shaft, the group arrives behind a grating in a robot workshop, where Dr. Nerdnick is being held prisoner, with his body cuffed to an operating table. Mario points out that several Robo Troopas and Robo Shy Guys are guarding Dr. Nerdnick, but before Luigi can flee, Princess Toadstool insists that they stay and fight. Mario breaks open the grating and leads the charge with his friends against the Robo Shy Guys, while Bunsen frees Dr. Nerdnick with a screwdriver concealed within her chest. Dr. Nerdnick greets Bunsen in a bizarre language that only she seems to understand, and they make their way back to the grating. Meanwhile, one of the two Robo Troopas spots Mario's group and prepares to attack them, but Mario and Toad knock them out.
Just then Robo Koopa returns, and he asks himself which button he should be pressing in order to use a certain attack. Dr. Nerdnick gives an answer, which Bunsen interprets for him, and Robo Koopa presses the button he was looking for. This causes him to shoot an energy beam from his finger at Toad, trapping him in a force field. Robo Koopa thanks Dr. Nerdnick for his advice, and traps Princess Toadstool in a force field as well, although the others get away. As Mario, Luigi, Dr. Nerdnick and Bunsen escape down the shaft, Robo Koopa orders two Robo Troopas to guard Princess Toadstool and Toad. Robo Koopa then chases after the others, crashing through the wall in the process.
Mario, Luigi, Dr. Nerdnick and Bunsen run through Robo Land and manage to get away from Robo Koopa. When they stop for a moment, Mario asks Dr. Nerdnick as to how they can stop Robo Koopa. Bunsen interprets Dr. Nerdnick's answer for Mario and Luigi, simply stating that they can't. Robo Koopa then catches up with them, and proceeds to crush them by knocking over a transformer. Luigi figures that they're doomed, but Mario tells him that it's plumbing time, and they proceed attach an L-shaped pipe to a fire hydrant, which Luigi activates. The force of the water keeps the transformer from falling over, but through Bunsen, Dr. Nerdnick explains that they should retreat, because electricity and water will electrocute them. Mario, Luigi, Dr. Nerdnick and Bunsen escape down another hole, while Robo Koopa stomps his foot, causing the pipe to fall from the fire hydrant, and the transformer to fall on top of him, shocking him greatly.
Later, Mario, Luigi, Dr. Nerdnick and Bunsen arrive at a junkyard, where Dr. Nernick propses that he will build Mario and Luigi a robot suit of their own that can defeat Robo Koopa. Dr. Nerdnick dubs his new suit the Plumbinator, and proceeds to build it out of spare parts. The Plumbinator requires both Mario and Luigi to operate, with Mario in control of the upper body, and Luigi the lower body. Before they can leave, the Plumbinator topples over, with Mario concluding that he and Luigi could use more practice before they face Robo Koopa.
Back in the workshop, where Princess Toadstool and Toad have been chained up, Princess Toadstool tells Robo Koopa that Mario and Luigi are going to defeat him. Robo Koopa boasts that Mario and Luigi don't stand a chance against him. A Robo Troopa alerts Robo Koopa that the Mario Bros. are approaching, and leads him to them.
Outside, Mario and Luigi are waiting for Robo Koopa. Mario looks through a telescope from within the Plumbinator, assuming that Robo Koopa is too scared to face them, just as Robo Koopa makes his entrance. After Robo Koopa taunts Mario, Mario tells him to fight. Robo Koopa fire several Bomb Plants from his Super Toes, which Mario deflects with a fly swatter. Robo Koopa avoids the explosions, and charges at Mario with a giant fist from within his robo suit. Mario jumps out of the way, and Robo Koopa crashes into a wall.
The Plumbinator fires several eggs at Robo Koopa, but they prove to be useless. Robo Koopa tosses a lasso at the Plumbinator, and proceeds to pull it towards him. However, Luigi cuts the rope with a pair of scissors. Robo Koopa then tumbles back into the wall, grabs a girder, and tosses it at the Plumbinator, which leaps out of the way and onto a rooftop. Robo Koopa activates a jetpack and chases after the Plumbinator, eventually knocking it off a rooftop and down to a lower level of Robo Land. The impact of the crash destroys the Plumbinator, and soon Mario, Dr. Nerdnick and Bunsen find themselves being chased by Robo Koopa once more.
Robo Koopa activates a net and succeeds in capturing Dr. Nerdnick. Mario asks Robo Koopa to let Dr. Nerdnick go, but he doesn't comply. Bunsen then interprets a message from Dr. Nerdnick, stating that they don't need to worry, since the robo suit will run out of fuel unless Robo Koopa pushes a particular button. Mario can't believe what he's hearing, as Robo Koopa pushes the button, and is blasted out of the suit into the sky. Mario asks about what had happened, and Bunsen explains that Dr. Nerdnick made up a lie so that Robo Koopa would push the ejector seat button.
Back at the workshop, Mario's group, Dr. Nerdnick and Bunsen have gathered around the Robo Koopa's old suit. Bunsen says that the robo suit is a present from Dr. Nerdnick for Mario and Luigi, but Mario is hesitant due to the potential danger of the suit. Bunsen says Dr. Nerdnick agrees and states that he instead converted the suit into a robo pizza oven, as she proceeds to open the chest of the suit, revealing several cooked pizzas, which in turn causes Mario's group to laugh.
Animation and continuity errors