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Prologue (How It’s begins.)
The Story started in Onett, as Ness, Lucas, Claus, Ninten, Jeff, and Paula hanging out. When suddenly, It’s a strange blizzard at Onett. Several strange-looking figures went chaos on the other side of Onett. Ness, Lucas, Claus, Ninten, Jeff, and Paula go to investigate. [STAGE 1: ONETT BLIZZARD]When they reached somewhere, a large figure(Bowser) appears out of the shadow before them. It was Bowser who was opposing our heroes. He explaining as he watching the blizzard. [STAGE 2: VS. BOWSER] After Defeating Him, He escapes as the blizzard hardly blow the heroes away, and suddenly…It vanished. It’s all pitch white... What happen to Ness and his friends?
Chapter 1 (Ness Arrived at the Mushroom Kingdom)
After Landing to the field close to the Mushroom Kingdom, Ness wakes up. He only remembers before he blasted off that he was fighting Bowser. Mario spotted Ness and explained that Bowser teams up with the more powerful evil force. Ness agreed to join Mario to find out more what happened. [STAGE 3: MUSHROOM FIELD]. When they reached to the Mushroom Kingdom, they found some Dark purple clones of themselves and they have to fight them to pass. [STAGE 4: VS. DARK CLONE (NESS), DARK CLONE (MARIO)]. After the fight, the clones vanishes into dust. Ness is wondering why are they attacking them. Mario thinks that there's no time to wonder what happen there, and continues to the kingdom.
Chapter 2 (Trouble on Hyrule)
Lucas land on his head when he lands in Hyrule. Lucas wondering around Hyrule, Worried about What happen to Ness and Claus and the others after the strange Blizzard. [STAGE 5: HYRULE FIELD]. Lucas finds a franklin badge and the group of Monsters appears before him. Who was their leader? Medusa! Ninten appears before Lucas to help him out against Medusa. [STAGE 6: VS. MEDUSA] Medusa retreats and vows to clash again when they cross her path again. Lucas still wondering what going on, Ninten explains. They Explored around The Village of Hyrule explaining why the blizzard happens. But then, A Green Strange-Looking Dragon appears to destroyed the Heroes. [STAGE 7 BOSS: Gamadon] After the Fight, the townspeople think they are the new heroes, and they thinks so too.
Chapter 3 (When a heroic Pichu ventured with him)
Claus landed on the Green Grassy field, He saw a little pichu on the ship near by. Claus asked who is he, and where is he now. His name was G.P. and he answer "Side-Sea Hill Top". Claus Joins G.P. to save the Side-Sea Hill Top and get him back to his homeland. [Stage 8: Side-Sea Hill Top] Claus and GP finds someone named Irater The NeedleMouse. He said that he want to beat up random people for money. [Stage 9: VS. IRATER] It explodes. Claus and GP make it, but Irater dies. GP said that he'll goes to find things that he can make a coin for, and leaving Claus alone. Claus is still looking for the others [Stage 10: Side-Sea Hill Top]. When walking down the street, Claus noticed the Ship floating around the skies, he ran to check it out.
Meanwhile, Ness and Mario is in the strange side of the Mushroom Kingdom finding Bowser and Ganondorf planning. [STAGE 11: VS. BOWSER, GANONDORF] . Bowser and Ganondorf escapes to the portal and Ness and Mario uses PK teleport to find their next location.
The Intermission cutscene is about The Dark Swordman (Dark Matter) is in the Dark Realm laughing, saying that His plan was working.
Chapter 4 (The awaken spirit)
In this chapter, Kumatoro wearings a blue coat with a hoodie on, fighting the gangsters in the icy field. [Stage 12: Icy Field] Kumatoro got her a blue glowing orb with a star on it, and discover where Lucas is right now...To Hyrule!! Kumatoro finds the Portal that lead to Hyrule, but Waluigi blocks her way.[STAGE 13:VS. WALUIGI] Kumatoro defeats Waluigi, which blast off into the sky, and Kumatoro goes to the Portal to Find Lucas. Kumatoro teleported to Hyrule, but the dark copies came to attack Kumatoro and probably to kidnap her. [STAGE 14: Vs Dark Copy(Ness) Dark Copy(Ninten)] After defeating the dark copies, Kumatoro begins her search for Lucas. [STAGE 15: HYRULE VILLAGE] In the Snowy Chinese-like temple village, Kumatoro found Lucas and Ninten, and tell them that The villains sent the Dark Copies of themselves to destroy the world for them. Wario and Waluigi and Bowser Jr. appears out of nowhere in their new machine to stop them from their tracks [STAGE 16 BOSS: WaBowgi 2.0.]. The villains escapes and Kumatoro tell Lucas if he ok. But Lucas is sick and said that he have a cold. Ninten and Kumatoro think that they might find the cure and said to Lucas to stay here. [STAGE 17: CHINESE VILLAGE]. They eventually found the cure: The Holy Turnip, which make Lucas feel more powerful, now they gotta find the others.
Meanwhile, Claus is still at the city, and then, he found Jeff. Jeff told him that Dr. Eggman and Medusa captured him, and Paula. Claus agreed and tell that He need to find Ness and his brother, Lucas. They agreed and they find the SubSpace Ship putting out some Shadow bugs to morph as dark viruses. [STAGE 18: Side-Sea Hill Top]. After they killed the viruses, They found GP again. GP tell them that he know where Dr.Eggman hold Paula at.
Chapter 5 (The Trouble in vain)
Ness and Mario went to the Chinese village. Ness found Ninten, Kumatoro, and Lucas. The old man named Worth walk and tell the heroes that Medusa have kidnapped Mylan. This make Lucas mad, because he encountered Medusa in Hyrule before he was stated the hero. He also said that they need to go to Medusa's Lair and defeat her. They agreed and exit the Chinese Village. [STAGE 19: The Snow land].Meanwhile, in the Subspace Gunship, Waluigi, Wario, Bowser jr., and Bowser reported to Dark Matter, who was sitting on a throne, sitting next to Paula, Zelda, and Peach in a cage. Claus burst the roof with his "Masked Man" suit and fly into Dark Matter's throne. Dark Matter grabs his sword and begin fighting. [STAGE 20: VS DARK MATTER]. Claus is tired out of Fighting him, Dark Matter grabs a dark gun, and blasted him off the gunship and landed into a island, and the gunship fly off. Claus landed on the field near the dojo, and he went into it, and find Poo there. Poo knows that Dark Matter defeated Claus, he gotta help him. [STAGE 21: Dojo Field]. Claus and Poo find Zelda, Wounded and knocked unconscious. They tries to help her, but Dr. Eggman and Metal Sonic stops them before they waked her up. [STAGE 22: VS. Dr. Eggman AND Metal Sonic]. Metal Sonic and Dr. Eggman flies off, and Claus and Poo waked Zelda up and heal her. Jeff appears to them and Claus ask Jeff where had he been, and he answered that Dr. Eggman destroyed Side-Sea Hill Top because he think it's stupid. They followed them and find Dark Samus encounter them. [STAGE 23 BOSS: Dark Samus]. Dark Samus died and Claus, Poo, Jeff, and Zelda went to the portal to Mobius.
Chapter 6 (Mylan in Trouble!)
Ness, Mario, Ninten, Kumatoro, and Lucas found Medusa's Castle, and they went into there and find viruses guarding the castle. [STAGE 24: Medusa's Castle]. They killed the viruses, and they went into Medusa's Lair. They found Medusa, holding Mylan hostage. Medusa shoots a laser on the heroes, but Ness reflect with his franklin badge, and hit Mylan's Cage. Now they're ready to fight Medusa. [STAGE 25: VS Medusa]. The Castle collapses, and Medusa died, the heroes found Pit and he told them to follow him out of the castle and into the ship. [STAGE 26: Collapsing Castle]. They lived and the castle is destroyed. They found the Halberd Ship and ride on it and fly away.Meanwhile in Mobius, Claus, Poo, Jeff, and Zelda is found a Space Ship flying around the sky. They dodged as the spaceship crashes, they found Krystal survived and everyone else died in the ship. Krystal tell the team that she was looking for Fox and Falco, Claus and the gang find some badniks running around the city attacking innocent people. [STAGE 27: Mobius]. After destroying some robots, Claus uses his "Masked Man" suit and flew to the Egg Fleet. After dodging some missiles, lasers, and bombs, Claus reached the top of the fleet. He find Dr. Eggman in his new machine, Supreme Egg Fister, and it grab Claus. Before he could crush Claus, Jeff shoots a powerful missile to the Supreme Egg Fister's Hand, releasing Claus, ready for a battle. [STAGE 28 BOSS: Supreme Egg Fister]. After destroying the machine, Dr. Eggman flees, the heroes went back to earth as Mobius is exploded.
They flew to the Skies of Wonder, knowing that they'll be safe here. Mylan discovers a Vision that an unknown figure is attacking Dream Land. Claus, GP, Krystal, Poo, Jeff, and Zelda find the gang, and hear what have happen. They will join Ness' Group, but leave Lucas and Mylan behind babysitting Maria, who is Mylan's Daughter. They hop in the Halberd Ship and travels into space to go to PopStar.
Chapter 7 (The figures of the shadow)The team went to PopStar and travel to Almost Ruined DreamLand, which they find Kirby attacking the viruses. Kirby suggest that they need to kill all the viruses, so they can save Dreamland. [STAGE 29: DreamLand]. They reached to the Fountain of Dreams, which is the only way to restore Dreamland. When suddenly the figures reveals to be Olarx X, and his new recruit, which is Irater's robotic body, called Irater 2.0. It was reveals that Dr. Wily found his dead body and recreate him. Claus and GP knew that Wily is working for the villains, and ready to defeat them both. [STAGE 30: VS. Olarx X AND Irater 2.0]. Irater 2.0 drops the star wand while escaping with his injured body. Kirby grabs the wand and put it back into the Fountain, and restore peace to DreamLand. Ninten still believe the villains is still afoot. They try to reach back to the Halberd, but the dark clones of Meta Knight, Link, and Shadow. [STAGE 31: Vs. Dark Copy(Meta Knight), Dark Copy(Link), Dark Copy(Shadow).] The clones vanishes, and the heroes went back to the Halberd and went back to Earth.
While Lucas, Maria, and Mylan saw the invasion on Skies of Wonder, and the SubSpace Gunship. Waluigi, Bowser, Ganondorf, and Wario came to defeat the heroes. [STAGE 32: Vs. Waluigi, Bowser] [STAGE 33: Vs. Wario, Ganondorf]. After defeating the villains, The Gunship attacks, but Mylan and Lucas combines their powers to create a powerful shield and blocks the lasers, missiles, and bombs. When the Halberd came back, and Claus know that Lucas is gonna to lose, The heroes came to strikes the Gunship. [STAGE 34: SubSpace Gunship (Skies of Wonder)].But The Gunship is too powerful, but luckily, the laser and missile system is failing, and the ship retreats and leave the Skies of Wonder behind, and Mylan restore the skies with her wand. Ness know that someone more powerful is behind all this, and they must find him, and stop his plans.
Chapter 8 (The Unknown Threat Strikes)
Dark Matter is getting bored of striking worlds, and thinking that his plans works. He decided that it's time to check on the prisoners. But one of the minions came and tell them the bad news: Paula, and Peach is attempting to escape. when he reached to the cell, Paula brakes the hole in the wall, and Peach went off by using the arwings. Paula is going to fight Dark Matter for make her his prisoner. [STAGE 35: Vs. Dark Matter]. After trying to defeat Dark Matter, Ganondorf, who recovered after the battle, grabs Paula and Dark Matter put a helmet on her head, making her wear a suit of armor, which make her into a evil soldier. Ganondorf tell her to betrays the heroes and reported the remaining dark copies, and she's off to destroy everyone, and the villains laughs, knowing that the heroes won't remember her.
Paula was flying off to betray the heroes while her first location is Chill Village, when an snowball exploded on her. The Ice Climbers had thrown that snowball, while they playing a snowball fight. They noticed that she was a intruder, they had to fight her. [STAGE 36: Vs. Paula(The Subspace Knight Suit)]. After the Ice Climbers realizes that there's no end to this, due to that Paula is too Strong, Nana suggests that the Mask is controlling Paula, and they uses their hammer to destroy it, which make Paula back to normal and changes her back into her normal clothing. Paula explains the whole thing, the Climbers agreed and run to stop the villains. [STAGE 37: Chill Village]. After they left the village, the giant condor flying around to block the heroes. [STAGE 38 BOSS: GIANT CONDOR]. They fly on the condor to get into the next location, hoping to find the other heroes.
Meanwhile, Ness and the gang came to the ground, and found Dr. Eggman and Ganondorf are in the way. [STAGE 39: VS. Dr. Eggman, Ganondorf]. Dr. Eggman flew, but Ganondorf got another plans. Before he punch Ninten, Ganondorf saw the condor and it drops off the Ice Climbers and Paula. Ness is surprised to see Paula escapes out of the ship, and Ganondorf knew that plan don't work, and teleported into the unknown location. Paula told them they must find the way to defeat the villains, they agreed. [STAGE 40: Unknown Field]. Poo discovered that the Town over there is under attacked, so the heroes went and go save the villagers. [STAGE 41: That First Town]. When they reach the end of the town, A chained boulder attacks Mario, Pit, and Jeff, and the boulder is by Wario. They have to fight him and stop him, as Wario eats the garlic and transform into his alter ego, WarioMan. [STAGE 42: Vs. Wario(WarioMan Costume)]. They defeated Wario, and Wario want to join them because Wario believes that Ganondorf and Dark Matter own him money. They agrees and try to find the other 3 heroes.
While travelling out, Mylan is worried if Cosmo and Karina is safe soon. The Heroes is suddenly encounter of the dark copies of Zelda, Silver, and Pit. The copies is threatening Sonic, Tails, Knuckles, Shadow, and Blaze, and the heroes need to stop them. [STAGE 43: Vs. Dark Copy(Zelda), Dark Copy(Silver), Dark Copy(Pit)] After defeating the copies, Sonic explains that Dr. Eggman already destroy Mobius, and they went to earth to stop him. They have separated to look for clues. The first team is Ness, Ninten, Blaze, Paula, Zelda, Tails, Popo, Nana, and Poo. The second team is Mylan, Lucas, Kumatoro, Krystal, Sonic, Kirby, Knuckles, Wario, Shadow, Claus, and GP.
Chapter 9 (The Unknown Chaotic Clash)
Ness, Ninten, Blaze, Paula, Tails, Zelda, Popo, Nana, and Poo went to the strange place, and find more dark copies. They prepare to fight them off, and then Marth unexpected slashed most of them. The remaining copies fuses and transformed into a Giant Dark Copy Giga Bowser-like Monster. [STAGE 44 BOSS: Giga-Dark Copy]. They defeat the monster, and Marth reveals that this strange place is the Chaos Shrine. They went inside the temple, now knowing that the evil on their side...
Meanwhile In somewhere in Poke-Island, in the Unova Region, Victini wakes up, but his mind is blacked out. He only remembers that he was fighting, but cannot remember anything else. Meloetta finds him, and care for him. She wonders why Victini's mind cleared from fighting, they team up to go find the person who fought him. [STAGE 45: UNOVA REGION]. They went to the middle of a strange forest, they Encounter Meta Knight and Ike who is somehow landed into Poke-Island. They prepare to fight them, and tries to knock some senses at them. [STAGE 46: Vs. Meta Knight, Ike]. Meta Knight and Ike need to find the location of Olarx X and Irater 2.0 causing havoc. Victini and Meloetta notices the strange ship that was about to fly away, and they point at the ship, and Meta Knight and Ike followed them and get into the ship [STAGE 47: OLARX X'S X-SHIP].
They're in the temple, forcing to face many monsters around the hallway. They prepare to battle the monsters. [STAGE 48: CHAOS SHRINE]. They reached to the throne room, Ganondorf is sitting in his throne, waiting for the heroes to attack him. He attacks Marth, and about to finish him off. And then, Samus attacks Ganondorf and weaken him. The Battle against Ganondorf is about to begin. [STAGE 49: Vs. Ganondorf]. Ganondorf had been beaten again, but not quite. He transformed into his true form: Ganon. [STAGE 50 BOSS: Beast Ganon]. After they defeated Ganon, they found the hidden door next to the throne. They're in the sacred cave filled with crystals and they're greeted by the gang of monsters.
Chapter 10 (Irater's Bloody Revenge)
Mylan, Lucas, Kumatoro, Sonic, Krystal, Kirby, Knuckles, Wario, Shadow, Claus, and GP found a resting place, and then suddenly, the evil robotic army appears. [STAGE 51: Tokyo, Japan]. They destroys the army, but Irater 2.0 appears and kidnapped Maria and Karina. Mylan is afaid that he might hurt her daughter and sister, so she tries to use her starlight wand, but Irater 2.0 commands the army and laughs manically. He laughs so evilly and insane, but a schoolboy cuts one of his arm, and shoots him. The Schoolboy is Ujori Kasami, he heard that the robot freak is trying to take over his home-city. Irater 2.0 got so insane that he want to kill them all. [STAGE 52: VS. Irater 2.0]. Irater 2.0 got defeated and let Maria and Karina go, and escapes. Ujori vows to hunt him down for attempting to destroy Tokyo. Ujori joins the party, and they went to a restaurant so they can eat and rest.
Meanwhile, Irater 2.0 is planning a evil trick, but is stopped by Fox and Falco. Irater 2.0 released the monsters to distract them. [STAGE 53: Irater's Ship]. After defeating half of the ship, they hop into their arwings to destory the rest of the ship. They notice that there's another arwing, and Peach is piloting it. They find Irater 2.0 and ready to fight him. [STAGE 54: VS. Irater 2.0]. Irater 2.0's arm ripped off, and he shoots a missle at the heroes. Peach landed on a tree from Hyrule, and Link saves her from falling off a tree. Peach needs to know where she is, and Link told her that she's in hyrule. Peach tell him that she's is not from Hyrule, She's from the Mushroom Kingdom, and she need to tell the toads about the "Revloution"! But one problem? She don't know where she can go back there. Link can help her how to get there. [STAGE 55: Hyrule Field].
Meanwhile, The heroes went out to the arcades, where Kumatoro and Lucas playing a game, and Claus, Wario, Ujori, GP, Sonic, and Maria is eating. They heard the noise, and they need to find out. They find the arwings. Fox and Falco survived and tell them that Irater 2.0 is still planning. They already know, they chasing Irater 2.0 down.
Chapter 11 (The Chaos Cave)
After exlopring around the cave, Ness, Ninten, Blaze, Paula, Tails, Zelda, Popo, Nana, Poo, Marth, and Samus is almost captured by the possessed pirates, and they saw Mario is alright and fighting the pirates. [STAGE 56: The Chaos Cave]. After defeating the pirates, they find the entrance out of the cave, but it was guarded by another Supreme Egg Fister, this time it was one of the protypes! While got the giant robot distracted, Popo, Nana, Ninten, Marth, and Tails escapes and wait for the heroes to destroy the robot and got out of there safe. [STAGE 57 BOSS: Supreme Egg Fister Prototype]. Ness uses PK Flash on the robot, which completely destroys it, and they escapes back to the surface.
They had saw Olarx X's ship, and they had to follow it. [STAGE 58: The Road to the Olarx X's Ship]. They manage to get on the ship, and the robots already kidnaps Popo, Nana, Ninten, Marth, and Tails in the cage. The robots want to robotize the hostages for their leader, Olarx X, so they can take over the world with the league of robots and dark copies for Dark Matter. After they discuss their plans, Irater 2.0 shows up, capturing Fox and Falco. However Fox shots Irater 2.0 in the back, and he and Falco escapes. Irater 2.0 having his robotic parts repaired, forcing the robots into the heroes [STAGE 59: The Robot Ambushing]. After destroying the robots and freeing the prisoners, Irater 2.0 decided to use a last-pitch effort by turning the robotic demonic beast called Irater 2.X and Olarx X teams with him. [STAGE 60 BOSS: Irater 2.X]. [STAGE 61: Vs. Olarx X]. After destroying Irater 2.X for good and defeating Olarx X, the ship is about to blow up, so Ness, Ninten, Blaze, Paula, Tails, Zelda, Popo, Nana, Poo, Marth, Samus, Fox and Falco escapes the ship and find Mylan, Maria, Lucas, Kumatoro, Sonic, Kirby, Knuckles, Wario, Shadow, and Claus at the forest, as they trying to find Fox and Falco this whole time.
Chapter 12 (The Blazing Fire in the Castle)
Ness, Ninten, Mylan, Maria, Sonic, Kirby, Tails, Knuckles, Blaze, Shadow, Claus, Marth, Samus, Fox, The Ice Climbers, Falco, Zelda, and Paula manage to find each other in the forest. The teams have to split up again and have to leave some of the members behind.