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In the throne room of the castle, Mario and Luigi stumble upon Princess Toadstool interrogating Wooster about the whereabouts of her crown. After learning that Wooster doesn't know where the crown is, Princess Toadstool begins to panic, if she doesn't have that crown in time for the "re-coronation" ceremony, she won't be able to be princess for an entire year; meaning Mushroom Land will be completely under the control of the idiotic King Toadstool, who has just stumbled into the room with his tie caught in a jar of peanut butter.
As Wooster and Princess Toadstool begin helping King Toadstool get his tie loose from the jar of peanut butter, Toad suddenly rushes into the room, saying that Bowser has amassed an army in "World Three". Princess Toadstool suddenly sends Mario and Luigi out to battle Bowser and his army, thinking that Bowser was the one who stole her crown.
In a large field, Bowser is in the process of telling his Lakitu minion that someone's been robbing him, stealing Koopabits from him and even his crown has been taken. As Bowser tells Lakitu and the rest of his troops to be on the look-out for traitors, Lakitu snickers to himself and gazes at all the stolen riches in his cloud, aptly named Fluffy.
As Bowser begins organizing his troops, Lakitu spots Mario and Luigi spying on Bowser. Before Mario or Luigi can react, Lakitu begins trying to pelt them with Spiny Eggs. As Mario starts trying to flee from all of Lakitu's thrown Spiny Eggs, Luigi tries to battle Lakitu by jumping on a nearby cloud.
Before Lakitu can attack Luigi though, Luigi jumps on top of Fluffy, knocking Lakitu aside. Seeing that Princess Toadstool's crown is among Lakitu's stolen loot, Luigi grabs it, just as Lakitu grabs and puts on Luigi's hat. As Lakitu prepares to try and hit Mario with a Spiny Egg, Luigi convinces Lakitu to count all his treasure instead.
After a while of running, Mario, after stomping a Goomba, makes his way to a Warp Pipe, believing Luigi to be behind him. It is only when Mario reaches the Warp Pipe that he realizes Luigi is no longer with him.
Turning around, Mario is confronted by a hat wearing Bowser and his army. An angry Bowser begins to accuse Mario of stealing his crown, saying he better return it, or else.
Up above, Luigi is still sorting Lakitu's treasures as Lakitu, having somehow stolen Luigi's clothes, oversees him. Suddenly, Fluffy stops and Lakitu, after warning Luigi to not pull the escape hatch, which he almost accidentally did, asks Fluffy what's wrong. Fluffy replies that Bowser is nearby and says that he and Lakitu are supposed to report to him.
As Fluffy approaches Bowser, Luigi sees Mario and, thinking quickly, pulls open the escape hatch, dumping himself, Lakitu and all his stolen treasures down below. On the ground, Luigi finds Mario and, after digging him out of a pile of Koopabits, travels back to Mushroom Land with Princess' Toadstool's crown while all nearby Shy Guys and Koopa Troopas begin taking all of Lakitu's Koopabits while Bowser, having been bonked on the head by a falling Lakitu, lies unconscious.