The camera then shows a scene at Bowser Castle, where a Goomba is stirring a cauldron. A clumsy Koopa Troopa knocks him into the "soup". Similar to the scene in New Super Mario Bros. (the final battle), the cauldron shakes, bubbles, and explodes, revealing Goomboss. Pandemonium ensues as the reborn chiertain rampages through Bowser Castle.
Waluigi soon discovers that Goomboss has usurped Bowser's throne, and is planning to use the Scepter of Superiority to increase his Goombas by millions. Waluigi then embarks on a quest to steal the Super Scepter, enlisting aid along the way from Bowser Jr. and Shadow Mario.
Waluigi- The hero of this particular game and a horrible cheater. His goal is to steal the Scepter of Superiority and finally win the hand of Princess Daisy. He uses a new superpower called Cheating to great advantage.
Bowser Jr.- The first obtainable second-player character. He uses Paint as a weapon, covering the enemy in paint and whacking them as a missile. The Paint also has many other uses, like creating bridges, ladders and safe patches of floor.
Shadow Mario- The first third-player character. It is unknown who is wearing the disguise, or if it is alive on its own now. Shadow Mario shoots Shadow Balls as a projectile, turning enemies to his side for five seconds before they die.
Mario- A third-player character that can be obtained by defeating General Guy. His lifetime skill at stomping Goombas is very useful in the Goomba-ridden Dark Land. He also has the ability to become Balloon Mario when you make an "M" shape with the Wii.
Luigi- A third-player character that can be obtained by defeating General Guy. Although easily frightened, Luigi uses a flashlight to neutralize any Terekuribos in the Dark Land. He can also become Vanish Luigi when an "L" shape is made with the Wii.
Goomboss - The main villain and final boss. The chieftain of all Goombas and wielder of the Scepter of Superiority. Although he cannot wield the Scepter's full powers, Goomboss has made a fearsome Goombarmy of the most terrifying Goombas he can create. The Scepter also makes Goomboss the commander of various bosses.
Big Bob-omb - The first boss. He has complete dominion over the Bob-ombs, the main weapons in his battle. He takes great pride in his Mustache, which happens to be his weak point. Big Bob-omb blocks the way at Bob-omb Keep.
King Boo - The second boss. His subjects are the Boos. The Terekuribos in this game are Goomba souls raised by King Boo himself (under Goomboss's orders). He can only be damaged by Boos, but there are no Boo Mushrooms in his battle. Instead, the mystical Fountain of Death must be used to make the transformation to Boo Waluigi. The ghastliest of ghouls haunts Misery Mansion.
Petey Piranha - The third boss. Petey is the supreme Piranha Plant, and so controls the carnivorous plants. Formidable in tems of strength and durability, Petey's only weakness is the Paint of Bowser Jr. This walking plant is the roots of Piranha Palace.
Lakithunder - The fourth boss. Lakithunder is not confirmed to be supreme Lakitu, but he is powerful enough that he holds all Lakitus in his power. The fastest way to defeat him is to Cheat his lightning up into his Cloud and destroy it. The darkest Lakitu of them all is hiding in Cloud Castle.
Major Burrows - The fifth boss. He commands the Monty Moles, and they command the Bullet Bills, Banzai Bills, and King Bills. To defeat this surprisingly weak boss, you must use what would be called underhanded tricks. The Major is surrounded by his finest artillery at Fort Banzai.