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Mario ends up on a small cliff overlooking a clearing. He looks down and notices a familiar enemy: Mr. L. Mario is confused as to how Mr. L is even there, as Luigi is watching this too. Mr. L brings out his troops, who the team realizes are simply evil versions of Mario, Wario, and Waluigi. Mario jumps down, and the group introduces themselves with style. They are the Negative Squad, and they say they are the ones who wrecked Toad Town. Mr. L, who happens to be the leader, sends Mr. M to take care of Mario. During the battle, though, none of them can hurt each other. Eventually Mario must run away, and the team goes on through Moonview Woods.
Moonview Woods is overrun with Crazee Dayzees and Hyper Goombas. It also seems that the Negative Squad forced some Koopas into their service, as many Negative Koopas roam the area. Eventually, Mario reaches the Underground Lab, but he finds the only way in is either through a very low passage which none of the team can go through or via the main door with a keycard lock. He tries to search for the keycard, but comes up empty handed. Mario attempts to go back, and winds up in Moonview City. There, Mario meets up with Wario again, and they battle once more. The plumber defeats his arch-nemesis, and is about to leave when Mona comes along and gets outraged that Mario laid a beating to Wario. She nearly attacks Mario when she notices that Wario has gone missing. Mona asks Mario what he’s doing there, and he tells her of his predicament. Mona offers her help and joins the team, able to use her Crawl ability to get through low places. With her help, Mario returns to Moonview Woods, and he approaches the Underground Labs. Mona crawls under the low passage and finds a circuit breaker connected to the keycard scanner on the door, and reprograms it to disable the lock. The door opens, and Mario approaches to see what lies within...
Right upon entering the Underground Labs, Mario sees a huge swarm of Laser Guys flocking to the exit. It seems that the Negative Squad had locked it from the inside as well. Mario continues through the Testing Area, where fallen Laser Guys who suffered the Negative Squad’s wrath flooded the area. After going through many traps and puzzles, Mario finds a dead end with a lone switch. He pulls it, and it seems nothing has happened. But then he finds that a huge swarm of Laser Guys, brainwashed by the Negative Squad, were just then activated, and the crowd surrounds Mario, giving him no escape. He is narrowly rescued by a Laser Guy survivor of the Squad’s mass enslavement named Lazey. He joins Mario’s partner party, able to use his long range laser attacks to hit switches and reflect off mirrors. If Mario hits a laser, he briefly has a laser aura around him, speeding him up and hitting any normally unusable switches. Soon, Mario meets up with Mr. M once more, and they have a serious battle. Mario emerges the victor, and goes deeper into the Underground Labs.
He goes into the Executive Area, where a group of prisoners are being held. Guarding the area is none other than Mr. W, who patrols the section along with his troupe of Negative Koopas. In order to free the prisoners from the cell, he has to find four keys while avoiding detection from the guards. Mario learns their route and manages to avoid being found. He sets free all the Laser Guys and Koopas and begins to lead the huge escape charge. However, just as he is about to exit, Mr. W comes and stops the rebellion. Mario steps forward to challenge his arch nemesis’ alter-ego, and defeats him just as he did to Wario. Mr. W flees with all his Negative Koopas, and continues on while all the captives escape to freedom.
The next area is the Manufacturing Area, the place where all the research and designs by the Testing Area are put into reality. In order to get through, Mario must hit a series of switches to rotate the mirrors to hit a solar panel to open a door. Using Lazey’s laser ability and Mona’s electric powers, Mario is able to configure the mirrors to the long path heading for the door. He proceeds to the main section of the area, where conveyor belts and other factory stuff abound. Mario just manages to make it through the maze of moving floors and rising platforms, when Mr. Upside Down L shows up and prepares a battle with Mario. The plumber defeats the dark Waluigi, and goes into the final area, the Command Area.
Here, Mario finds something cruel: the brainwashed servants are forced to battle against each other to find defects. At once, the Negative Koopas and Laser Guys attack him, but Mario sweeps them aside. Mario makes a disguise like a Koopa and takes one’s gear, and heads into the arena, storming aside all of the Negative Squad’s henchmen. After these battles, Mario searches for the head office, and comes face to face with the mastermind: Mr. L.
After a bit of mocking, Mr. L charges at Mario, but the Green Thunder is beaten just like the rest of his squad. Mr. L runs to the arena, with Mario in hot pursuit. The crowd cheers as Mr. L enters. He taunts Mario some more, and pulls out a control for his “ultimate weapon”: his master computer system called the LES. He commands LES to attack Mario, and the whole crowd goes in a huge uproar over Mario’s imminent defeat. Mario gets his game face on and challenges the computer. Though LES is armed with an infinite artificial intelligence and a huge weapons array, Mario defeats Mr. L’s last trick. Mr. L swears revenge and nearly bolts out, but after LES’ defeat, all of his servants came back to their senses and block Mr. L’s passage. He bumps into the crowd and a strange yellow shard drops to the ground. Mario picks it up, and asks what it is. (Actually, his partner asks what it is.) Mr. L tells him of the Element Star, an ancient mystical object that brings ultimate power to the beholder. It was long ago split into five pieces, the Electric Piece, the Fire Piece, the Ice Piece, the Earth Piece and the Iron Piece. But just as fast as Mario obtained the Electric Piece, Mr. M comes in and swipes it. He and Mr. L leave in an instant, leaving Mario confused. The Laser Guys congratulate Mario for freeing them, and the chapter ends.
A scene comes to Bowser’s Castle, where Peach is still being held. Bowser barges in and steals Peach’s brooch. He opens it up, and out comes a red shard: the Fire Piece. He hands her back the brooch, and hands it to the person who just entered: Mr. W. Mr. W laughs and storms out of the room and Bowser says he’ll keep Peach just for the fun of it. Bowser leaves in a hurry, and Peach sighs and looks outward, calling for Mario.
Another monologue comes, saying:
“I recalled our first exile. We had a member of the clan so power-hungry that he attempted to conquer the entire world, threatening to use his bizarre powers obtained through a chemical accident. We sent him out into another dimension, using a trickery of his own powers. He swore that he would have this world destroyed one day.
“We can only fear he will have his revenge soon.”
The scene goes to the main square of Moonview City, where all of its residents and the freed Laser Guys are thanking Mario for his outstanding work. Then an older professor comes and tells Mario that he must collect the other fragments of the Element Star before the Negative Squad does. He says that the Negative Squad already has the Iron Piece, but he knows for sure that the Ice Piece is at Mt. Frostbite. He also mentions that the Negative Squad said something about collecting the Fire Piece at Bowser’s Castle. Mario remembers that Peach was kidnapped, and leaves in a hurry for Toad Town.
When Mario takes one of the ways to Toad Town (Two blue pipes appear, one from Moonview City and one from the Underground Labs.), he finds the place fixed up, but strangely deserted. He goes up north, and notices a strange happening. Small pieces of pure white are appearing everywhere more and more frequently as he goes on. It is also occurring to the sides and in the sky. He finds where all the Toads have gone, to a spot where almost everything is white with spots of reality. They are all gathered by a single Toad who went too far and is simply an outline of black and white. Nobody knows what it is exactly, but they are sure it is growing at a steady pace. Mario asks one how to get to Bowser’s Castle, and he says it is south of Toad Town, on the Lava Sea. The passage leads to Gray Bluffs, and soon enough Mario will be able to see Bowser’s Castle. Mario heads south to rescue Peach and get the Fire Piece, and prepares for his imminent battle with his ultimate rival: Bowser.