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The story starts with Pyrouge finding a brown book with a star on it. He opens it up and gets sucked into the 2-D Mushroom Kingdom. Meanwhile Parakarry delivers a letter to Mario's house that Luigi reads (didn't see that coming now did ya!). The letter says that a convention is being held at the Castle to disscuss the Kingdom's defenses, and Mario has been asked to join the meeting. Pyrouge lands on Jolly Trail where he notices that he is now 2-D. He presses forward, fighting Goombas until he reaches Peaches castle. At the same time Mario appears at the Front Gate. Realizing that this is THE Mario, the same one from his video games and the wiki he's aways on, he greets himself as his biggest fan as giant clumps of dark matter fly at them. They then see their arch nemisee, Darkly and Bowser on top of the castle. It turns out the letter was a hoax and the 2 red heroes get blasted to kingdom come!
They wake up in Goomba Town where the Goomba Mayor (really Goompapa) greets them and teaches them action commands (Note: While Mario still uses hammers and jumps, Pyrouge uses Fire and Punches). Pyrouge explains to Mario how he got to the mushroom kingdom and says that he needs his help to get back to the Elemental Plains. Mario accepts and the two head out to the Goomba Town Museum, where they meet none other than Goombario and Goombella. They are currently dating and decide to help Mario & Pyrouge. Here the player can chose either one of the Goombas and their tattles differ, but still give the same neccesary information. The other Goomba then teaches about switching out (Press X to Split up. When they split up, Mario and Pyrouge can use their diffrent partners in and out of battle. Mario and Pyrouge have diffrent partners they recruit as the adventure goes on. Goombario or Goombella joins Mario.)and gives them the Power Jump and Power Punch Badges and explains how Badges are used, They then set out for Goomba road. In Goomba Road, Mario and Pyrouge fight goombas and use splitting up to solve puzzles. They eventually meet up with the Goomba Lord, son of the Goomba King, who tells them of Bowser and Darkly's plan to take over the Kingdom. He then attacks the two with the aid of Blue and Red Goomba. Mario and Pyrouge take them down easily as they let down a bridge to Toad Town.
Meanwhile, Peach is lamenting about how much she hates being kidnapped. She decides to not let it get the better of her and snoop around the castle. She uses the secret passage from the first game to get to Bowser's current location. He talks to Darkly how it was ingenious to break the Star Medalions before giving them to Bowser's elite troops. Darkly tries to convince Bowser to let him infuse his minions with darkness, but Bowser says that it would give them a good excuse to sue him. Darkly then asks if the Guardians of Fire and Ice would keep the medalion pieces well protected, because they are Pyrouge and Mario's only hope of beating them, while Bowser reassures him. Peaches sneaks back and tells Mario, via text message, about Bowser and Darkly's plan.