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The game starts off with an opening sequence in a style similar to the other Paper Mario games, describing the main plots of the previous three games. Then it describes about how all those events would come together someday, when a disturbance from the so-called “Dimension of Abandoned Souls” emerges. It created a portal that could connect to any time and place. It was said that all the lost souls in this place were too scared to go near it…but one wanted revenge on those on the other side. This is that story…a tale of vengeance, love, and true evil…
Then the game starts, and after selecting profiles and stuff, then the story begins. Parakarry comes and delivers a mail letter to the Mario Bros. house (just for old time’s sake). Luigi comes out, collects the mail, and reads it to Mario. But no, it is not a friendly invitation from Princess Peach! It seems to be a warning letter…addressed to Bowser?! It says that Peach has a rare object and that Bowser must kidnap her during the royal procession…or else. In a state of panic, the brothers rush over to the castle, only to find that the procession is going on right now!! The player takes control of Mario, and enters the castle. Unfortunately, Mario doesn’t get a second to react as Bowser and Kammy Koopa rush into the palace, but tire down as the enter, saying that their transport is broken. Shortly after, Bowser’s alter-ego clone, Dry Bowser, enters and threatens to eat the princess if Bowser and Kammy don’t get up. Just as they do, however, Luigi enters and jumps on Kammy and Bowser, knocking them back down, but gets hurt jumping on Dry Bowser’s horns. Then Mario steps forward, and challenges the undead beast. An introductory battle takes place, where Luigi introduces Jump and Hammer Commands. Mario eventually defeats the skeletal king.
After the battle, Dry Bowser runs away, but it turns out the whole battle was more of a distraction, as Bowser and Kammy had already flown off with Peach, and it seems Luigi has gone missing as well. Mario exits the castle, and sits by a fountain, knowing his mission has failed. A Goomba named Goombierre comes and sits next to him, lamenting of his lost dreams. The two get in a “conversation” and after a while Goombierre joins your party. The two get up, reinvigorated, and walk out to Rogueport, the main hub of the game.
There are many things to do in Rogueport, providing every convenience there could be. After walking through the town a bit, Mario notices a group of Toads gathered around a manhole. They reveal a horrible truth: there’s a monster ravaging the sewers, and it’s kidnapped a huge group of Toads! Alarmed, Goombierre boldly says that Mario is not afraid, but soon notices Mario backing away. After the Toads tease the two for being chicken, Mario and Goombierre fall in anyway. The Toads realize there is minimal hope of the two ever coming back, and so they leave. But it turns out Mario and Goombierre survived the great fall, and are in a small room with a river of sewage. The two go into a nearby pipe, and the first chapter begins.