Crimes R Us
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King Koopa and his Koopalings are all onboard the Doomship, and are flying over a town somewhere in the Real World. Bully Koopa announces that they're about to reach a prison, and Koopa is quite pleased, noting that a prison is the only place on Earth with their kind of people.
Down below, in the prison courtyard, a large, muscular prisoner is playing a game of basketball with some of the other prisoners. When one of the other prisoners laughs at him for failing to make a shot, the larger prisoner rolls him up into a ball, and shoots him through the net. When the large prisoner challenges the other prisoners into beating him, they run away.
Suddenly, the large prisoner experiences a tremor, and looks up to see the Doomship firing at a guard tower. Bully then descends down to the prisoner from the Doomship on a rope ladder, and asks if he's Crimewave Clyde, Public Enemy #1. The prisoner assures him that he is, or else he wouldn't have been sentenced to jail for 12,423 years with no parole. Bully tells Clyde that his father is giving him a pardon, grabs him, and brings him onboard the Doomship.
Surrounded by the Koopas, Clyde wants to know who the Koopas are, and what they want with him. When they arrive at Castle Koopa, Koopa explains his background to Clyde, who can barely believe what he's hearing. He further tells Clyde that he busted him out of jail so that he could teach the Koopalings all the tactics he used to commit crimes. When Clyde wants to know what he'll get out of this whole ordeal, Koopa tells him that he can keep half of whatever's stolen. Unaware that Koopa had crossed his fingers behind his back, Clyde agrees.
Later on, the Doomship pulls up above the First Mushroom Bank, and Clyde prepares to teach the Koopalings their first lesson in crime: bank robbery. Meanwhile, Mario and Luigi are going on a walk through the Mushroom Kingdom, where Mario points out that the clouds in the sky sometimes resemble things, including Princess Toadstool. Luigi first spots a cloud that barely resembles their Aunt Maria, and then the Doomship, which he at first mistakes for a cloud.
Realizing that the Koopas are pulling a bank heist, Mario and Luigi scramble to find power-ups. Mario finds a Super Leaf to become Raccoon Mario, while Luigi uses a Fire Flower to become Fire Luigi. Inside the bank, the Koopalings seize the Mushroom people there and steal the valuables they have on them. Just as Bully forces the banker to toss all of his Gold Coins into a sack, Mario knocks the sack away from Bully with his tail, and it hits Hip and Hop. Luigi shoots a fireball at Big Mouth, Kooky and Cheatsy. However, Kootie Pie uses a fur scarf she stole to wrap up Mario with, while Bully sprays Luigi with a fire extinguisher. With the heroes down, the Koopalings retreat to the Doomship.
Back at Castle Koopa, the Koopalings are beating each other up, while Clyde tells them that they failed lesson one in crime. He then proceeds to lesson two; getting rid of the good guys.
At some later point, Mario and Luigi come out of a Warp Pipe in Desert Land, where they hear a voice crying for help. The voice leads them to a Mushroom boy, who explains that some ugly monsters stole his lunch money, and directs Mario and Luigi to the pipe they escaped through. Once Mario and Luigi travel down the pipe, Cheatsy comes out of the hiding, thanks the kid for leading Mario and Luigi down the pipe, and actually returns the stolen lunch money.
Mario and Luigi come out of a pipe in a maze underneath Desert Land, which closes behind them. They then hear Clyde laugh, and turn to see him with Big Mouth, who tells them that they're trapped. Just after Big Mouth and Clyde lock them in, Big Mouth briefly opens the door to let in a Boom Boom that will "keep them company". The Boom Boom chases Mario and Luigi into some quicksand, with no visible ways of escape.
Mario angers the Boom Boom by clucking like a chicken, and lures him into jumping into the quicksand. As the Boom Boom jumps at him, Mario jumps into the air and hits a Jump Block containing a Super Leaf. As Raccoon Mario, Mario picks up Luigi and flies across the quicksand.
In the Mushroom Kingdom, Clyde explains to the Koopalings that he's now taught them everything he knows, and sends them out to commit crimes. Big Mouth uses a Ptooie to hold up a Mushroom lady, while Kooky steals the coins in her purse. Big Mouth then threatens Kootie Pie into handing her stolen loot over to him, and they get into a fight.
After returning to Castle Koopa, Bully reads from a list everything that they mangaged to steal. When Big Mouth uses his Ptooie to demand a stolen yo-yo from Bully, Clyde gets mad, exclaiming that the Koopalings shouldn't steal from each other. Hip and Hop take to Clyde's advice by stealing wallets from his pockets. Although Clyde is frustrated, Koopa is proud of his children, and announces that they need to pull the "crime of the Mushroom Century".
Bully wonders if they'll rob the ruins of the Mushroom pharaohs, while Cheatsy thinks that they'll pilfer the pyramids of the Koopahari Desert. Kootie Pie thinks it's getting rid of Princess Toadstool, but Koopa shakes his head at all their ideas before unveiling his plan: stealing one billion gold coins from the Mushroom Kingdom Treasury.
Down in the maze, Mario and Luigi are finding themselves chased by Ptooies and Sledge Bros., and find themselves locked in a room with two Thwomps. Luigi is fairly worried, because he's certain that there's no possible way out of the maze.
At the entrance to the Mushroom Kingdom Treasury, Crimewave Clyde hands a Bob-omb to Kooky, telling him not to light it until he says go. Kooky then lights the Bob-omb and handcuffs it to Clyde's ankle. When Clyde asks what's going on, the Koopalings explain that they're following Koopa's orders, and that they didn't plan on giving him anything. Not able to take the Koopalings' antics, Clyde jumps into a pond, dousing the Bob-omb's lit fuse.
In the maze, Mario and Luigi are trying to dodge the Thwomps. Just when Luigi tells Mario that they're finished, Clyde busts down the door, begging for Mario and Luigi to get him back home. Although they're angry at Clyde, he promises to help Mario and Luigi in stopping the Koopalings from robbing the Mushroom Treasury.
At the treasury, Bully uses a Bob-omb to blast open the front door, while Hip and Hop use a Chain Chomp to open a barred window. Kooky unleashes a Firesnake, which busts a hole on the roof, while Big Mouth blasts a hole in the wall with his Ptooie. Once the Koopalings enter the treasury, they begin loading up bags with coins. When Bully and Kootie Pie open a vault door, they are shocked to see Mario, Luigi and Clyde waiting for them on the other side.
Up aboard the Doomship, King Koopa hoists up a platform supporting two money sacks. However, upon opening one sack he sees his children all tied up and gagged. The second sack falls open on its own, revealing a lit Bob-omb, which blows away part of the Doomship, creating fireworks around it, causing it to retreat from the Mushroom Kingdom, and Clyde smiles.
Later on, Mario and Luigi return Clyde to his jail cell. Luigi remarks that he's never seen anyone so happy to actually be behind bars. Clyde responds by stating that his 12,423 year sentence with no parole is a lot better than one more day with the Koopas. Upon hearing Clyde's remark, Mario mentions that Clyde's lucky because he didn't have to face the Koopalings on a bad day.
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