Pyrouge's story starts with Pyrouge and Sparker in his castle bored out of their minds. While wondering what to do, an odd black portal opens. Although Pyrouge knows the SMART thing to do would be ignoring it, he also knows the FUN thing to do would be to go in and see where it leads!. However only Pyrouge makes it through before the portal closes. Before he escaped the portal however, he saw a blury red figure pass through as well. He ends up in an odd forest where he finds none other than Luigi. Pyrouge asks where Mario is and he replies that he went in the same portal Pyrouge came out (in the same gibberish that's used in Mario & Luigi games).Before they can look inside however, it disappears! While they're talking, 2 goombas come and start harrasing Pyrouge. Luigi just wants to ignore them, but Pyrouge remembers how good it felt to squish (or punch) his first real goomba and he wants to do it again. This starts an introductory battle that teaches timed hits,and magic moves (which uses the same SMRPG fighting style). After the battle Pyrouge says that Luigi should come with him to the castle and Luigi joins his party.

They fight their way through goombas and koopas until they get to Mushroom Square, and the castle. They meet the princess who welcomes Pyrouge back to the kingdom. Pyrouge tells her and Toadsworth of his perdicament and decides to look around the Kingdom for any evidence. Peach then wants to join, which Toadsworth resents, but Pyrouge promises he'll put his life before the princesses and they set of for adventure. Before they leave, however Toadsworth tells Pyrouge about "Partner Commands", special techniques used by party members. Pyrouge can have 2 partners follow him and use L and R to use their commands. (By the way, A is jump, B is punch, hold B for flame shot, X for map, Y for items,Start for menu, Select for Tips, and Touch Screen for shortcuts) Luigi can create thunder and peach can float over gaps. Then Pyrouge and Co. set out towards their next destination.

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