EMERGENCY NEWS FLASH! Princess Peach has been kidnapped! While enjoying a nice walk with Mario, the beloved ruler of the Mushroom Kingdom was whisked away by an unknown assailant. How could this happen with Mario around? According to eyewitnesses, the walk was going swimmingly when Mario and the princess spotted smoke billowing out of Peach’s Castle. The mustachioed marvel immediately jumped into action and sped off toward the fire. The moment he left her side, the princess vanished! Who’s behind Princess Peach’s disappearance? Who’s behind the attack on Peach’s Castle? Are the two incidents related? Didn’t Bowser Jr. once think Princess Peach might be his mother? Looks like Mario’s going to need all the Mega Mushrooms he can find to get to the bottom of this mess!
Mario starts looking for the princess in the fields near the castle. She is nowhere to be seen, but luckily Mario finds that the hidden mushrooms that he finds can give him special powers. What he cannot find is the princess however, so, Mario goes first underground and then to the giant mushroom kingdom in the sky. He still does not find Peach, but he comes face to face with Bowser Jr. in the first tower. Mario gives him a sound beating but Jr. is soon back on his feet running away with the princess again.
Mario follows the kid straight to his castle, where Bowser Sr. comes to see what all the noise is about. Mario is quick to send him falling in the lava pit below, burning him down to his bones. Jr. is still running away though, this time he takes the princess beyond the desert.
With little hope of stopping Bowser Jr. any time soon, Mario must make his way through perilous traps under the burning sun, jumping over the heads of Pokey worms. Eventually he reaches the castle, where he finds more traps waiting for him. This time Jr. calls upon the help of a sand worm in order to gain some time to run away.
The next stop is in a forested land, where Mario must also swim underground in Cheep-Cheep infested waters and on to the next tower and the spooky forest, not to mention his first encounter with the annoying Skeeters. In this land’s castle, apart from more spiky traps, Mario is confronted by a huge Cheep-Chomp fish.
Jr. runs towards snow land, and Mario slips and slides behind him whilst avoiding snowballs and other pitfalls. Mario goes inside the spooky hut to recover from the cold, only to run into Broozer the punching ghost. He must again walk knee-deep in the snow before he reaches the castle, where a giant man-eating plant tries to eat its daily lunch.
Mario follows Bowser Jr. between the canyons of the rocky mountain land, where tornadoes and high tide on the land’s beaches are common. Jr. has two towers to hide into here, but again he is no match for Mario, so he keeps running away.
Running through the sewer pipes to reach the castle, at the far end Mario is attacked from behind by an armored tank, which is driven by a mole called Monty. Monty resorts to all sorts of tricks, pushing buttons to shoot bombs and bullets. Every time he is hit, Monty pushes a button to add another turret to his arsenal, but in doing so he is only delaying the inevitable explosion that he is soon to experience.
The landscape turns gloomy red as Jr. gets close to home. Inside the castle, the skeleton of Bowser Sr. awaits Mario, who is quick to make him fall in the lava once again. Mario corners Jr. who has his escape route blocked by a sea of lava. As Mario prepares to rescue the princess, Jr. activates a bridge that rises from the lava below to create a new path towards his castle fortress, in the hope that he can hide within.
Mario must travel inside a volcano and evade the erupting lava before he can reach the castle, where he must go forward through the most devious of traps. In the castle’s hall, Bowser Jr. is waiting for him, with Sr.’s corpse lying at his feet. Jr. suddenly brings a pot of magic in the room and throws the bones of his father inside it. Poof! Bowser is back from the dead, and now both father and son attack the plumber.
With Princess Peach looking on from a nearby ledge, Mario stops and throws back Jr.’s shell attacks whilst evading Sr.’s fireballs. Once again, he presses the big red button to send the big turtle down to his doom. Mario can now re-embrace the princess, whilst the young Bowser drags his unconscious father to a safe place while probably already plotting his next scheme.