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Mario and Luigi are summoned by a Toad named Rowho to stop a group of roudy Goombas who captured Princess Peach. Apon defeating them, they realized that the Goombas weren't the actual masterminds of the plot and face Seek Peek, a big Goomba with a big ego. Apparently he wanted to make his claim to fame by defeating Luigi once and for all. After easily dispatching him, a sinister man named B appears out of nowhere, Claming that it is time for him take vengeance on his foes. Luigi notes that he speaks just like Count Bleck. D creates a portal and sucks Mario,Peach, and all the Goombas inside. Luigi is blasted away into the sky. D laughs, and states that "it's almost like the begining..."
Luigi awakes drifting in space. As he drifts, he has flashbacks of various scenes from Super Paper Mario and Paper Bleck (two of the game's predecessors). Finally, he comes to rest on the planet Cubulo. After exploring it for a while , he comes apon Merlon, who is being attacked by Soopa Strikers. After defeating them, Merlon thanks you and remembers you from Super Paper Mario. He learns of what you underwent at D's hands and says that D seems to be some sort of Bleck impersonator, not Bleck himself- Bleck is safe and sound with Tippi at Honk Honk Port. He says that Bleck himself is the only one who would know how to deal with D. Merlon flips himself and Mario to Honk Honk.
Once they arrive, Merlon gives Luigi a tour of the area. When they arrive at Bleck's house, he becomes panicked apon learning of D. He says that he can't find Timpani, his wife and he refusesto assist Merlon untill she is found. Luigi goes to the top floor of Howye's Hardware Store and finds Timpani there. After a tearful reunion, the two procced back to Bleck, who says that he if this Bleck impersonator, is so much of him , he may be weakened by a Mystery Star- the substance from which the Pure Hearts were forged. Bleck advises that Luigi go look for him in the town of Candellwhick. Timpani decides to go with Luigi go look for him in the town of Candellwhick. Timpani decides to go with Luigi on the adventure, on the adventure, joining his party. Bleck and Merlonled over to Smiley Sam, a Lakitu who files a Cheep Cheep balloon. Sam agrees to fly them to Candellwhick,and the adveture begins.
Sam drops Mario and Timpani off in the gloomy town of Candellwhick. After defeating a group of pesky Koopa Troopas, Timpani uses her Wiimote Pointing Ability (that she had in Super Paper Mario) to reveal a hidden door. They walk through and find Bulb cowering in the darkness. He saysthat someone tried to steal the Mystery Star from him, and in his desperation, shattered the star . The released energies blasted seven pieces of the star away into the sky, but Bulb still had the eighth piece. Bulb says that he saw where another piece went: Wordly World Forest.
Chapter One:Wordly World Worlds
Mario and Timpani arrived at the Wordly World Forest (which looks like World 1-1) After Dispatching hundredsog pesky Goombas, Luigi and co. run into the first boss, a weak and mostly harmless purple-shelled koopa Troopa named Koomba. Koomba says he's tired of being trampled by more powerful people and uses a Mega Star to grow huge. He tramples Luigi to within an inch of his HP when Luigi finds a Mega Star and easily takes out Goombo.
D is talking to his henchmen (Mira(a shapeshifter like Mimi), Chugger (brute force like O'Chunks), and Nastasia). Nastasia apparently thinks that D is Count Bleck returned from the dead. D fakes being in love with her to make her do his bidding. B demands that Nastasia "bring out the prisoner." She does so, and the prisoner is none other than... Francies. D tells Nastasia to do her thing, and Francis undergoes the same process Luigi underwent in Super Paper Mario. He becomes... THE GREAT NERR! tells The Great Nerr to destroy Luigi, and he sets off...
Luigi and Timpani, having punted Koomba, arrive in an ancient forest. They explore, and soon come upon The Great Nerr. The heroes get ready for a battle, but Nerr just laughs and says that his "new Francies" will deal with Mario. Nerr fades away and a dozen Tiptrons appear and attack. Luigi jumps and stomps his way through them and reaches Nerr. The geeky chameleon-turned-evil-henchman attacks- he's the second boss. Luigi manages to defeat him. Nerr turns and flees. He uses his abilities to fly over a fast-moving river, but a "flip box" is drawn around him. The box flips, and Nerr is now just Francies... without his powers.. over a deep river. With a final cry of "NERRRRRRRRRR!" Francies plummites away, The second Mystery Star frangment appears.
Nastalia flips into reality next to D, dragging a sopping wet Francis with her. D seems surprised that Francies is alive, and says that he had meant for "that bungling fool" to drown when he took away his powers. D starts sulking, and says that Mira can deal with Luigi.
Chapter ll:The Seas of Soakland
Mario and Timpani return to Honk Honk with the Mystery Star, Bulb leads them to the next portal, to an underwater world called Soakland.
Upon entering, the two meet a Cheep-Cheep who guides them to the box. The Cheep-Cheep says that the Mystery Star fragement is in the box, but instead, it's a bob-omb! When luigi isn't hurt, the Cheep-Cheep transforms into Mira and says that Count B will destroy them. Mario and Co. continue on nonchalantly and explore the depths. At last, after a grueling search, they find the Mystery Star Fragment. But Mira appears and attacks! Third boss fight. She shapeshifts randomly into different enemies, and can only be hurt in Goomba form. Mario finally knocks her unconscious. She flips out of the demension and reappears again in an instaht, like Francies/Nerr, and loses her powers, Luigi tries to get to the Star Fragment, but an explosion rocks the Seas of Soakland. A hole appears in the wall. The water, Timpani, and the Mystery star get sucked through! Luigi holds on, and faces his next (incredibly easy) boss- a familar foe... Koomba! He's very angry that he lost last time. However, without a Mega Star, He's easily jumped on and kicked away. Timpani and the Mystery Star Fragment wash up, and Luigi siezes his prize!
B is very angry. He yells and shouts at everyones present (Chugger, Nastasia , and a powerless Mira). Nastasia says that he shouldn't have taken Mira's powers away, because now they're one less minion! But B simply yells at her, saying that he "tried to get more minions by brainwashing that green loser and the pink girl but all they did was go fight in the Glitz Pit!" and flips away.