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The two find themselves in an area called the Old Old Sewers, an old sewer system teeming with Goombas and Koopas. After battling their way through the sewers, they come to a little area with shops and such called Sewerville. They talk to the old Goomba mayor of the town, and he says that lots of Dry Bones have come up and taken some Koopas. Goombierre tells him of Toad Town’s similar situation, and that they might be related. The mayor sends you off to the east area of Old Old Sewers, and you come across some of the Dry Bones that have been kidnapping the Koopas. However, you come across a huge gap, with the switch to lower a bridge on the other side. The two find themselves in a messy situation: a group of Dry Bones in their dead form are blocking the way back to town. Mario looks around, and notices a little house hidden from view. The two go inside, and meet a Koopa named Koopella, who is in a bit of a situation herself. Some Dry Bones were about to kidnap her, so she put out her shell so the Dry Bones would think she is in it. They fell for it, but she can’t come out without her shell on. The two look for her shell, and find that the Dry Bones who were blocking the way back to town happened to have her shell. But just as Mario is about to get it, the Dry Bones wake up, along with the head Dark Bones, and the squadron attacks. Mario and Goombierre easily defeat the undead Koopas and retrieve Koopella’s shell. They return to Koopella’s house, and give her the prized shell. She hops out and joins Mario’s party out of thankfulness.
With Koopella’s help, the new team of three is able to cross the gap and gives chase to the Dry Bones squadron. They work their way through the long path until they reach the huge Dry Dry Fortress. After grueling challenges, they reach the commander of the Dry Bones armada: the gigantic Mecha-Bones, a huge mechanical Dry Bones operating the whole fortress through his attachment to the fortress wall. The sinister beast congratulates Mario on his progress, but says confidently that the little plumber cannot stop him. But after a long and tiring battle, Mario proves the Mecha-Bones wrong, and demands the Toads to be freed. But it turns out that there were no Toads at all in the fortress, simply captured Koopas turned into Dry Bones servants. Mario bops the mechanical commander one last time, and Mecha-Bones self-destructs, dropping a strange key. The team returns to Sewerville, and tells the mayor about the whole incident. It turns out the key opens up a secret door to the lair of the Piranha Plants, known only as the Piranha Kingdom. Mario seeks out the door, and opens up the huge door, entering the Piranha Kingdom.
The Piranha Kingdom seems to be the opposite of the Old Old Sewers. While Sewerville and surrounding areas were filthy and small, yet welcoming, the Piranha Kingdom was huge and modernized, with a cold, empty feel. Almost immediately upon entering, the team gets ambushed by a group of Piranha Plants, and narrowly fights their way to victory. They decide it must be the Piranha Plants behind this whole operation, and after the royal parade of the Piranha Plants, this turns out to be correct: the leader, Petey Piranha, is sucking away the Toads’ life force to power the kingdom! Aghast at this discovery, Mario attempts to attack the Piranha king, but is stopped as Petey sends all the Piranha Plants in the crowd to destroy the hero. The crew once again narrowly escapes impossible odds, but find that Petey Piranha has already been taken back to his mighty castle. The Piranha Plants notice Mario’s absence, and quickly find the plumber. But just before they obliterate Mario, the door to the Piranha Kingdom bursts open, and the huge army of Dry Bones floods in, waging war with the Piranhas, with the Red Bones as its’ leader. The Frost Piranha general and the Red Bones organize their armies into perfect lines, but sends them both back into a chaotic pile. But it seems the Piranhas have not forgotten about Mario, as they have sent a Putrid Piranha out to deal with him. After Mario beats this poisonous plant, a Dry Bones comes up and reveals the reasons for the chaos: the Dry Bones army has long been at war with the Piranha Plants, and they actually weren’t kidnapping Koopas, they were simply taking those who volunteered for the army to their fortress to officially making them members. He also tells him that this entire battle is actually a distraction so Mario can safely enter the castle. With the support of the Dry Bones, Mario proceeds into the castle to defeat Petey Piranha and end this all.
The Piranha castle is even more advanced than the city itself, and filled to the brim with deadly traps. There is even a dungeon that imitates endless levels of the classic Mario Bros. game (this is actually more of a minigame, as you must exit by going through one of the pipes the enemies come out of.) Eventually, you come across a strange area with an upside-down door. Confused as to what to do, Mario presses on, and eventually meets a spirit who grants him the Rotate Dimensional ability, where Mario can rotate certain walls and floor areas. With this new ability, Mario can proceed through all the dangerous puzzles and traps the Piranha King set in his castle. After battling his way through all sorts of enemies and solving puzzles (mainly utilizing Koopella and the Rotate ability). Mario finally reaches the tower where Petey Piranha resides. The huge plant monster shows no remorse at his kidnapping of the Toads to power all his high-tech devices and engages Mario in a great battle royale, doing everything from summoning a protective horde of Piranha Plants to actually swallowing the plumber. But in the end the great beast is no match for the power of Mario, Goombierre and Koopella. Petey Piranha, on the verge of losing it all, reveals his true motives. It turns out that this was all revenge for the Toads sending such a huge amount of soldiers down to exterminate some Piranha Plants, simply because they were scared. Petey Piranha frees the Toads, who overheard, and soon Dark Bones comes up and they all make a three way pact- the Piranha Plants will remain neutral so long as the Toads and Dry Bones keep the peace. They all agree, and Petey Piranha brings Mario and Dark Bones over to the grand balcony, and makes a major announcement to all the Piranha Plants and Dry Bones remaining in the streets. He says only five words: "The Thousand-Year War ends." With this, everyone goes into a huge, joyful uproar, and the chapter ends.
The scene goes over to Bowser’s Castle, where Peach is imprisoned in a high tower. She sighs and looks over the bleak landscape, not knowing as to why she was kidnapped. She thinks it might be just like normal, but for some reason she feels it is not the reason this time. She walks around a bit, and then sees a strange phenomenon in the corner. She attempts to look at it, but it quickly disappears. After wondering a bit, she overhears a conversation between Bowser and a strangely familiar voice. She remembers who it might be, but decides it is impossible. With this scary thought in mind, she falls asleep and the scene ends.
Then a short monologue takes place. It says:
“It all started when we saw that great object in the sky. It looked, to describe it best, a red bulb. It came closer, and closer, and it was evident it was some sort of spacecraft. And it had no intention of stopping. I alerted the king of our town, because for some reason I was the only one who noticed. It was indeed a spacecraft, and as it came closer we could see similar bulb-like life-forms inside. They seemed to be in a muted panic, as the spacecraft caught on fire. Everyone cleared away, and we all waited for the explosion…that never happened. We looked where it was to crash, and it was instead making a huge hole. We knew not to think of it, but we were glad that we were safe.
“How wrong we were.”
The scene shifts to Mario in front of Piranha Castle, where Petey Piranha and Dark Bones are saying their farewells. But then Mario asks how they are to get back, and Petey Piranha tells him of a secret room only accessible through Mario’s Rotate ability. From there all worlds are accessible, or so it is said. There is even a pipe leading to the Piranha Kingdom from there, and one to Sewerville and the Dry Fortress. Mario leaves in search of the room, and eventually manages to find it. He takes the first blue pipe (The second, third and fourth lead to Sewerville, Dry Fortress, and the Piranha Kingdom respectively.) and he ends up in a house of Toad Town. They get out and find that a huge group of Toads, thankful for the daring mission, have been out in search of Mario, and they sweep him off his feet, carrying him through the town. After a while, Mario is let down, and they praise him for all his heroic deeds. But a very shaky Toad comes and alerts Mario of another danger: Luigi has gone to an area called the Micro Zone and hasn’t been back for a week! Astonished, Mario asks for which way the Micro Zone is, and the Toad tells him it is east of Rogueport, across Asphalt Desert. Mario stocks up on supplies and heads out to rescue Luigi once more from the clutches of a giant house.