Bowser and Mario are once again fighting over the princess, Mario uses a special attack which weakens Bowser. The evil Koopa King tells Kamek to beat Mario to death. Kamek thinks that is not an option and that they should just let the plumber go. Bowser just grabs Kamek and throws him to the ground, the Magikoopa just flies away without saying a word. Then he tells Bowser Jr. to attach Mario with the Clown Car, but Tim J. Koopa thinks he should get to ride first and that he was older and should get more respect. Bowser tells him to run off, but Tim just throws a rock at Bowser Jr. and grabs Bowser and throws him. Mario escapes, but Bowser Jr. and Tim are alone in battle.
- Bowser Jr. (only in Chapter 1-1)
- Luigi (second player)
- Bowser (after convincing him to join)
Chapter One: Bom-omb Factory
Bowser Jr. loses the battle against his relative. After that, Bowser Jr. searches for his father, but he cannot find him. Suddenly he sees Mario and Luigi are carrying Bowser, in a mansion far away King Boo sees Mario and Luigi and he sends out Boos to capture Luigi. Mario notices Luigi was not beside him and then Bowser woke up. Bowser asked Mario what happened and the plumber answered. Then they see Tim Koopa fly in the clown car to the Bom-omb factory.
After they get in, they must find Tim to stop the madness between Tim and Bowser Jr.