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Mario takes the short path to Gray Bluffs, a dead forest filled with Boos and pale enemies. He makes his way to the edge of Gray Bluffs to come face to face with the Lava Sea. Mario sees Bowser’s Castle, but the bridge is up and there seems to be no way to cross the lava. Mario hits a nearby switch which opens up a hidden path somewhere in the woods. Mario follows the way intrigued, and after a while finds himself at a little village of mixed peoples, including Bumptys, Twilighters and Yoshis. One of the Bumptys welcomes him to the place called Highcrest Town, filled with people who appreciate the nearby Dead Woods’ “beauty” and spend a lot of money moving in. He also mentions a visitor from Sarasaland. Mario looks around the town and notes the gatekeeper who says Mario has no business beyond that point. He continues on and meets up with Daisy, who says she’s there on vacation. Mario tells her of the fact that Peach was kidnapped, and Daisy joins along to help Mario find her. Using Daisy’s ability to float across gaps, Mario manages to reach the castle.
Mario ventures through the halls of Bowser’s Castle, defeating all the enemies that come in his way. After a while Mario reaches the central gardens, where he sees a huge locked tower. Finding no way to open it, Mario presses on, going towards the back of the castle. He comes across a room where he finds a key, but a wall quickly comes down and blocks the door. As Mario continues on, he reaches the place where prisoners are kept, and finds that his old partner, Lady Bow, has been taken. She says the only reason she can’t just go through the bars is that Dry Bowser came along and put a curse on her, but if she can get out she will regain her powers. Mario finds a hidden passage leading to the control room, and hits the switch to open the jail cells. Unfortunately, this not only releases Bow, but all the other prisoners as well, and they all go off in a huge uproar, waking up Billy, the Bullet Bill guard. Mario returns to Bow to retreat the area, but is then stopped by Billy, who rounded up all the others. Mario fights Billy, who is eventually beaten. Bow thanks Mario and joins his team, being able to hide Mario from enemies and allowing him to pass through blocked passages. Mario passes through the blocked off door, and opens it from the outside. All the prisoners leave the area, opening the drawbridge and escaping. Mario, back in the central plaza, is able to reach the dungeons, where a prisoner told him of a key to open the door to the tower. Ever closer to his goal, Mario goes down into the dungeons.
Though at first the dungeons weren’t all too special, it turns out that the area is actually the lava filtration system for the Lava Sea. They see a few bridges to cross the lava, but they are moved out of the way, so Mario has to venture through the area to find switches to move them. After moving all three bridges, Mario meets up with Dry Bowser, the apparent overseer of the dungeons. He remembers Mario from the castle raid and challenges Mario to a battle. However, Mario overcomes the skeletal Bowser and obtains the key to the central tower. However, upon obtaining the key, the lava in the area begins to rise as the filtration system breaks down. Mario quickly escapes and heads to the door teach Bowser a lesson.
Mario unlocks the door and ascends the tower, defeating all of Bowser’s goons along the way. He goes to the elevator block, but finds that a strange block is in the way. Mario searches around the castle and finds the switch to make the block disappear. He ascends once more, and finds that two more of these blocks are in the way. After finding both the switches, Mario is finally able to go up to the topmost room, where he meets up with Bowser, who tells him that Peach is in the room just past there. Mario and Bowser engage in a battle, just like old times, but ultimately Bowser loses. Mario continues on to the stairs, and opens the door to Peach’s cell. Immediately upon entering, Peach rushes over to Mario, and thanks him for saving her. Mario asks about the Fire Piece, and Peach opens up her brooch and gives him the Fire Piece, and the chapter ends.
The scene goes over to an unknown base, where Mr. M is simply walking about when Mr. W enters. Mr. M says that the project is going smoothly, and orders Mr. W to head out to Mt. Frostbite, where he knows for sure the Ice Piece is. Mr. W leaves and Mr. M laughs to himself, saying that Mario’s doom awaits him…
Then another monologue goes on, saying:
“We found the signature of the spacecraft. It traced back to a strange satellite very far off in the cosmos, very literally on the other side of the universe. We made a huge spaceship that could propel us that far, attached to a rig that could carry all of our people. Another was built to carry supplies. After all, we wanted revenge on those who destroy our planet. Besides, how menacing could a simple satellite be?
“And yet I still worry…”
Mario is preparing to leave the room when a huge rumbling comes, and something is heard downstairs. Mario goes through the door and sneaks over to a hiding spot, and sees Mr. L depart from a Brobot-like airship, asking Bowser where the Fire Piece is. Bowser says that he got knocked out and that Mario probably already took it and Peach. Mr. L goes in a rage and says that Bowser will be severely punished, and drags him into the airship. He sends out two guards to watch over the entrance while they prepare for takeoff. Mario rushes out and fights through the guards to board the airship, with Peach at his side. However, upon entering, the guards managed to sound an alarm before passing out and loads of the Negative Squad’s goons come to the boarding dock. They all pile on to Mario, preventing him from moving. Peach then cries out for Mario when a few guards take her away. Soon the guards overpower Mario in his desperate attempt to escape, and he slips away…
Mario wakes up in a holding cell of the airship, and sees Mr. L coming up to mock Mario in his attempts to collect all of the pieces of the Element Star before the Negative Squad. He points out that they already have three pieces, including the Fire Piece they stole from Mario, and the other two are very close in their grasp. Mr. L laughs and walks off, leaving Mario alone in the nearly empty holding cells, with the only other few captives being Fuzzies. Mario calls out for Peach, but he gets no response. Bow comes out and suggests that she could just get Mario through the walls, but it turns out Mr. L made precautions against that and put spectral deflectant on the bars. Mario simply waits in the cell until he hears a crash from above, and Wario drops in through the hole in the ceiling he made. He mockingly congratulates Mario on his being captured, and pounds another hole in the floor to the storage area. Mario drops down the hole to see Wario about to pound another hole, saying he knows how to get out of the castle. He completes the ground pound, and sees that the airship is already in flight. He yells out as he falls all the way down to the thickest part of Moonview Woods, and a huge dust cloud comes up. Mario continues through the airship, to find Peach, reclaim the Fire Piece and make Mr. L pay once and for all.
Mario advances through the more familiar Negative Koopas and the more recent Negative Fuzzies, presumably the reason for the Fuzzies being hostages in the holding cell. After a while, Mario comes to the elevator, and finds the airship is divided into 5 levels, with Mr. L being on floor 1 at the top. However, floors 1 and 2 are restricted access, requiring a keycard to proceed. Mario first goes to floor 4, which is the holding cell area, with guard quarters on the other end. All the guard quarters are empty, though, and Mario sees why: all of them are by the hole in Mario’s cell that allowed him to escape. One of them spots Mario, and he winds up in a massive progressive enemy fight, going through all 20 of the goons. After they all lay defeated, Mario searches around but finds no keycard among any of them. Mario goes up to floor 3, where the managing section is. After searching through the hallways, all Mario can find of note is a door to the upper storage area, but has a huge gap and can only be reached high above. However, since the airship is in motion, wind is flowing up through the gap. Daisy comes out and says her parasol can’t absorb wind, but she remembers Peach getting a wind parasol at some point. Mario continues to search through the rooms, and finds a secret passage in a seemingly average room. It leads to a passage where Peach is being specially held. Mario opens Peach’s door, and she runs up to Mario, thanking him for freeing her a second time, this time kissing Mario on the cheek. Peach says she refuses to be separated from any of the group from that point on, and joins your team, able to use her wind powered parasol to float across wind. (She cannot float across gaps with no wind, however.) With Peach at his side, Mario continues on to unlock the secrets hidden in the airship…
Using Peach, Mario and the team is able to quickly get up to the upper storage room, which has an opening to the second floor. Ironically, they find an elevator keycard right there. They see that the second floor is where the pilot operates the craft. Mario rushes over to the elevator, but finds that only the pilot and the Negative Squad leaders have the special card to get to the top floor. Mario takes the path to the pilot’s room, and attacks him. The pilot puts up a decent fight, using basic Negative goons and unique ways, so far as to making a working humanoid fighter out of them. However, Mario overcomes him and takes his special keycard, going up to the top floor to settle things once and for all.
When Mario arrives on the top floor, Mr. L is chasing Bowser around the area, and eventually traps him near the front. Mr. L turns around, expecting the pilot, but is somewhat shocked when he sees Mario coming up. However, he simply says he would love Mario to see this, and so he uses a Negative Zone on Bowser, and he flies shortly up into the air, before landing in inverse coloring. Mr. L orders his new creation, which he calls Negative Bowser, to attack Mario. Negative Bowser uses his Negative Zone powers to amp up his attack, and sometimes shoots smaller Negative Zones at Mario. Despite this, Mario manages to defeat the fiend, and Bowser regains his normal coloring in a massive, inverted explosion. Bowser looks around, confused, but then the ship gives a huge lurch and Bowser flies out the window, and Mr. L topples into the wall. A grunt comes up and says that the controls are busted due to the explosion, and that they’re going to crash. Mr. L and a bunch of grunts rush over to the escape pod, realizing that they don’t need the airship since the whole point of it was to deliver stuff so they could destroy Mario. And since they believe Mario would be destroyed by the crash, they see no purpose in the supplies. They blast off, leaving Mario in the falling airship. They see the ground approaching, and Daisy rushes over to the busted window and tells everyone to hang on. Almost right when the airship crashes into the ground, Daisy jumps off and floats safely to the ground, which happens to be in the middle of Highcrest Town. Mario notices all the citizens rushing over to the crashed airship, which is blocking the entrance. Some workers come up and say that they’re going to help get it out of the way. However, they state that it will take a while, and tell Mario to come back at a later time. Mario goes off to explore the town, and upon going into the east area, sees a bunch of people near the gate, who then turn around and see Mario, whom they state just ran through the gate with a bunch of Fuzzies just a while ago. Mario goes over to the gate to investigate this strange scenario, because as Mario will find out…he’s about to be in the midst of a huge crisis…one that could shape just how the battle between him and the Negative Squad will unfold.