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Mario arrives in the Dead Woods, filled with more powerful Dark enemies, like Dark Puffs and Pale Piranhas, but still contains Clefts. After going through the area, Mario comes across a large gap that Daisy is not able to cross. But just as Mario turns back, he sees a rustling in the bushes and Waluigi comes out to ambush them. He says he and Luigi still have a score to settle, and battles Mario and his crew. After a short battle, Mario defeats Waluigi and he falls to the ground. He asks Mario why he would be in a place like this, and he explains to him about his quest for the pieces of the Element Star, and about the recent situation, where a Mario look-alike kidnapped the hostage Fuzzies aboard the airship. Waluigi says that an adventure was just what he was searching for, and he joins your team, despite Luigi being there. He uses his long-jump ability to cross big gaps, so he can easily leap the canyon in the way. With Waluigi on his side, Mario continues on.
(Just to explain this, Waluigi’s long jump does not surpass Daisy’s parasol. It’s complicated, but I’ll try to explain. Imagine a large gap, just like the one mentioned, with a cave in one of the walls. Mario and Co. are on the side without the cave. Now, if you use Daisy, she will float steadily forward, but also down. Since she is going down, she obviously cannot reach the other side of the gap; she can only reach the cave. However, if you use Waluigi, he does a very long jump, but after it is done, he falls straight down. If you use it at the very edge of the cliff, he can reach the other side, but not the cave. In simpler terms, imagine a rectangle. The team is at the top left. Daisy can land at the bottom right corner, but Waluigi can reach the top slightly away from the edge. It’s kinda hard to grasp, but if you think about it, it makes sense.)
Mario arrives at the Master Tree, a gigantic tree in the depths of the woods. He sees a Fuzzy hopping along, saying that a man in red just like Mario passed by with all his friends earlier. He says that the red man may also be trying to brainwash the tribe leader, Fuzzy Buzzy. Mario heads into the tree, and finds it has been converted into some kind of headquarters. Right when he enters, he sees the mysterious man in red, who of course is Mr. M. He spots Mario and mutters to himself, but runs over to an elevator, which he then locks. Mario is forced to go the normal way up the stairs, which leads up to floor 2. Mario finds a map and sees the tree is now a 10 level base, with floor 10 being the top of the trunk. The elevator only leads to floor 4, while a second one there goes all the way up to 10. Mario solves many traps and puzzles to ascend the steps, along the way seeing Fuzzies in large experimental tubes being sent some strange glowing liquid. Eventually Mario gets to floor 4, where he sees Mr. M loading some Fuzzies into those tubes. He turns to see Mario, and simply laughs and presses a few buttons on a control panel. Something happens with the Fuzzies, and soon they bust out of the tubes, slowly transforming. After a short while they all turn into Smorgs, and fuse together to make the Smorg V1. Wordlessly revealing his plan, Mr. M heads off through the second elevator, leaving Mario to deal with the Smorg. After a tiring battle, Mario defeats the monster and continues on, knowing he must stop Mr. M’s obvious plan…to use a Smorg army to obliterate everything.
Mario goes on through the passages of the Master Tree, battling individual Smorgs along the way, who can fuse with other Smorgs to boost their attack power. After opening the way to three stairwells, Mario arrives at floor 6, where he sees a huge Fuzzy with a Buzzy Beetle shell on his head in a huge test tube. Mario busts him out with his hammer, and Fuzzy Buzzy falls out, still slightly dazed. He sees Mario and says that he was doing all of this, and attacks him. Mario manages to beat the half-Smorg Fuzzy, and soon he returns to his senses. He goes up to try and beat Mr. M for his torturing of the Fuzzies, and Mario gives chase to him, battling all the Smorgs and Negative Fuzzies in his way. He soon arrives at floor 10, where Mr. M awaits him. He shoots a blaze at Fuzzy Buzzy, knocking him to the floor. Mario hops over to his evil counterpart, and challenges him to a battle. Though Mr. M has many of the same attacks as Mario, as well as the power to use a Negative Zone, Mario defeats him. He lays knocked out on the floor, dropping the Electric Piece. Mario picks it up, at last having two pieces of the Element Star, and heads over to the cannon at the edge of the tree, which blasts him back to Highcrest Town, and the chapter ends…
The scene stays at the top of the tree, however, where a bunch of Smorgs hop out of the elevator and see Fuzzy Buzzy and Mr. M unconscious. A few carry Fuzzy Buzzy back inside, but most of them stay by Mr. M. They say something to each other, and start to crowd over Mr. M. In the flood of Smorgs, Mr. M says that all is going according to plan, and that Mario is wrong about an army of Smorgs…
Back in Highcrest Town, Mario tells all the residents of Mr. M’s plan to destroy all with the Smorgs, which were actually modified Fuzzies. He says that Mr. M would probably destroy Highcrest Town first, since it was right there. Mario notices the workers are having trouble breaking down the airship. But then Toadia comes along and sees the giant Luigi head airship. She asks the workers why they would ever destroy it, and suggests that they simply move it. The workers all agree on this, and head to the side to try and move it. The mayor calls Mario over, and gives him 100 coins in return for his efforts and basically saving Highcrest Town and maybe even the world from total destruction. Mario heads back to see the workers, but then notices one of them and Toadia has gone. Mario heads back to where the mayor just was, and finds that he disappeared too. Mario keeps going around, noticing that people are constantly disappearing whenever they leave his sight, and soon all but the innkeeper and shop manager have gone missing. He goes in the east part of town and notices that a bunch of Smorgs are holding Toadia, and crowd around her. They all back off, and Mario sees that Toadia now has a different coloring and has a slight blue aura around her. She says that this is only a demo of the true potential of the Smorgs and effectively the Negative Squad. She warns that if Mario keeps interfering in the Negative Squad’s plans, then the same fate will happen to him as all the other citizens of Highcrest Town, and he will serve the very people he was hopelessly fighting, and will be consumed by the power of Mr. M and the Smorgs. She is then taken away by the Smorgs, and Mario gives chase to them, realizing there was much more at stake then he thought.
Mario rushes through the Dead Woods, now infested with Smorgs who only serve to impede him. He quickly arrives at the Master Tree, where the interior has been completely ripped apart due to the destructive nature of the Smorgs. They also cut down the power lines, because the lights keep flickering on and off, thus hindering Mario’s progress even more. The stairs have been blocked off, so Mario takes the elevator, hoping the remaining power will be enough to get him up to the top. As predicted, it only gets him up to floor 2, so he climbs out of the elevator and navigates the shaft, using hidden switches to create platforms so he can get to floor 4. After a long while, he opens the door and finds a huge group of Smorgs awaiting him. They all start to flood onto him, when something blasts into them and they fly off. Mario sees that it was Billy, the prison guard from Bowser’s Castle. He says he was chasing Mario all over the place to get him back to the castle, but Mario tells him the castle has already been cleaned out and Bowser is nowhere to be found. Billy sighs and says he came all this way for nothing, but Mario suggests that he could be of help to him. Billy refuses at first, but gives in eventually. With Mario being able to use Billy as a controlled projectile, he is able to progress further to uncover the truth behind the whole plot…
Mario attempts to use the elevator to get to floor 10, but the power has gone way down and the stairs are blocked off. However, Billy gets an idea to use the Electric Piece to connect it to the power core. He takes the map and finds a shaft on this floor that leads to the power system. Mario gives him the Electric Piece, and navigates him through the shaft, eventually reaching the main power core, where he inserts the Electric Piece. Immediately the whole place turns light and the power goes way up, but an alert sounds saying the power system is overloaded. Billy removes the Electric Piece and finds it sent enough power to last them through the journey. Mario is about to go to the elevator when a huge group of Smorgs come and form together to make the Smorg V2. Mario runs for the elevator, and narrowly escapes the Smorgs attack. However, at about floor 8, the elevator stops, and Mario climbs out, expecting to have to navigate the shaft once more. However, he finds that the Smorgs have stopped the elevator, and so Mario goes to destroy it once and for all. Though the Smorg V2 is far more powerful than the V1, Mario still manages to overcome it and the elevator continues on to the top of the tree.
The elevator arrives at the top and Mario steps out to brace what he might see. However, all he does see is Mr. M, but notices he has been Smorgified. Mario steps back but Mr. M launches a string of Smorgs from seemingly nowhere and grabs him back. Showing off his new control over Smorgs, he battles Mario, sure he will destroy him with his immense power. But Mr. M and his Smorgs prove no match for Mario, and Mr. M, enraged, flies off using his Smorg power. All of the remaining Smorgs revert back to the citizens of Highcrest Town, and Mario explains what really happened, that Mr. M was actually planning to convert all the people in the world into Smorgs he would use for his own power. Mario, along with all the other citizens of Highcrest Town, are stuffed into the cannon as a Fuzzy resident of the Master Tree lights the fuse. They all blast back to town, and the chapter ends.
The scene goes to another unknown base (as the previous one was the Master Tree), where Mr. M is giving his report to Mr. L. Mr. L goes into an outrage about him losing the Electric Piece, but then is told about Mr. M’s new control over Smorgs, and says that he has thought of a new plan. He sends Mr. M off to make sure Mr. Upside Down L is doing his job in the Nothing Zone, and to check on Mr. W at Mt, Frostbite. Mr. M simply sends off a group or Smorgs to do both jobs, and says he has better things to do. Mr. L just sighs and leaves, worrying if the Smorg thing might be a problem.
Then another monologue comes (what did you expect?), saying:
“We stayed around to enjoy the last days on our planet. My wife and I had already packed everything we would ever need, but she still said it wasn’t enough. She said the planet was the only thing that could make her truly happy, but I simply said that our kind must not deserve the planet if the gods decide it must be destroyed. She just looked back at the mountains nearby, where she grew up as a child, and then said words that meant so much at the time you would think it was from the gods themselves.
“’Maybe the one we exiled has managed to trick the gods…’”
Then the scene goes back over to Highcrest Town, where the mayor and pretty much everyone are expressing their thanks for saving the world twice, though one of them points out that technically he only saved them once. Then they all hear a huge shout from the entrance, where Toadia is rejoicing over the airship moved to the side as a tourist attraction. She says she will run it like a museum, and will charge everyone 500 coins to go on a full tour. But she whispers to Luigi that it doesn’t apply to him, since the museum is made in his honor. Mario leaves for Toad Town, and once he arrives, still finds people in somewhat in a state of shock from the Nothing Zone invading the town, but they have recovered somewhat. However, it is nearly to the center of town, and so they urge Mario to hurry up with whatever it was he was doing. Mario heads to the entrance to Mt. Frostbite, where the adventure amps up for him…