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Part 1: The Invasion.
In mushroom castle, a festival was going on. Mario came down the hall to peach's room.He walked in, and saw it was empty.He realized something was wrong. But before he could completly think it through, the bell rang. He sighed, and went into the arena. all of the audience were cheering very loudly, especially Kirby, one of mario's close allies. Mario didn't realize why the comotion was so intense, untill he saw who his opponent was. It was Geno, an old friend of Mario. They decided to start the battle, as the audience cheered louder then before. (stage 1: vs mario/geno:playable characters: geno/mario) They shook hands. but before they can see the next battle, Kirby jumps down to them, and points at a giant airship. The trio decide to escape (stage 2:race to the finish: playable characters: Mario,Kirby,Geno)
Fox was flying the arwing through space when he saw a wormhole seemingly sucking up the planets he and his crew have encountered. Naturally, he figured this couldn't be good. He tried shooting at it with the arwing's lasers. This proved to be inefective, so fox became worried. Then he saw Dark Matter standing before him, as he had created the wormhole. Dark Matter get's inside the arwing and faces fox. (stage 3: vs Dark Matter: playable characters: Fox) Fox defeats dark matter and goes through space, parkouring on different platforms, searching for help. (stage 4: at the edge of space: playable characters: fox) Fox arrives at an abbandoned space ship that lays on a chunk of the moon. Fox peeks inside and sees aliens raiding it. The aliens are being controlled by dark matter. Fox chases Dark Matter to free the aliens from his control. (stage 5:race to the finish:playable characters:fox) Dark matter activates a bomb inside the ship. The next shot shows fox's trophy flying through space.
Mario,Kirby,and Geno are in a forest searching for help. they see an arwing aiming it's blaster at them, and fires. The trio dodge the blasts, as the cockpit ejects, who is revealed to be Wario, who is holding up krystal's trophy in victory. The three battle Warıo (stage 6: vs wario:Playable Characters:Mario,Geno,Kirby) Mario,Kirby,and Geno take Wario down. However, a wolfen swoops down and takes krystal's trophy. the team decides to follow the wolfen.
A young boy is running through the forest. This boy is Lucas, who is lost and looking for a home.(stage 7: forest: playable characters:lucas) he sees a hut and decides to go inside. (stage 8:hut:playable characters:lucas) he goes down to the basement and sees kremlins raiding the basement of it's bannanas and decides to help fend them off. (stage 8: basement: playable characters:lucas) lucas starts to get tired and can't fend off the kremlins. suddenly, a large shadow casts over the kremlins. the shadow lands in front of lucas, and is revealed to be Donkey Kong.(stage 9:defeat 45 enemies:playable characters:Donkey Kong,Lucas) DK puts Lucas on his back and searches for diddy.
Back at the castle, the festival was being trashed. Toad, who was running the festival, tries to fend off hostile forces. (stage 10:defeat 30 enemies:playable characters:toad) suddenly, he sees a car pull over and from the car ejects Proffesor Layton. the 2 decide to take down hostile forces together. (stage 11:festival:Playabe characters: Proffesor layton,toad)
In skyworld, Pit is seen training, Magnus appears, and they begin to spar (stage 12:vs magnus/pit:playable characters: pit/magnus) they see palutena is missing.they split up to look for her.
Pit flies down towards a desert, where he sees a trophy flying down towards him. he revives the trophy, as it appears to be fox.Fox and Pit find a castle and explore it.(stage 13: desert castle:playable characters: Fox,Pit) they see that the castle is being raided. They see Marth fighting off koopas and decide to help him. (stage 14: defeat 45 enemies:playable characters:Marth,Fox,Pit)
In a forest, Meta Knight is fighting off waddle dees. (stage 15: defeat 20 enemies: playable characters: Meta Knight) he sees a figure walking through the forest. The figure is Steve. The two have a duel, but see a horde of zombies coming their way. (stage 16: defeat 35 enemies:playable characters:steve,meta knight)
Pit,Fox, and Marth escape the castle and see a car pull over. out from the car comes Proffesor layton and toad. The five see medusa coming at them. (boss 1:Medusa: playable characters: Pit,Marth,Fox,Proffesor Layton,Toad)
Mario,Kirby, and Geno are walking through the forest. they see Bowser jr. and his army of cosmic clones. (stage 17: defeat 20 enemies:Playable characters: Mario,Kirby, Geno) Bowser jr. is about to finish them off but Magnus arrives to help. (stage 18: vs Bowser jr.: playable characters:Magnus) Mario,Magnus,Geno, and Kirby see a battleship and decide to follow it.
Pit,Marth,Fox,Proffesor Layton, and Toad are in the desert when they see a sword stuck inside a stone.Toon Link pulls the sword from the stone and sees the five. The six are ambushed by claus. (stage 19:vs claus:playable characters:Pit,Marth,Toad,Toon Link,Fox,Proffesor Layton)
Meta Knight and Steve are in the forest when they see Donkey kong and lucas. Meta Knight raises his sword at Donkey Kong (stage 20: vs Meta knight/Donkey Kong:Playable characters:Donkey Kong/Meta Knight) Diddy Kong comes in and breaks up the fighting. together, the team fights ridley. (Boss 2: Ridley:Playable characters: Donkey Kong,Diddy Kong,Lucas,Meta Knight,Steve) the Layton Mobile pulls over beside them.
Mario,Magnus,Geno, and Kirby jump up onto the ship and see Bowser laughing evily. He unleashes Peach and Palutena on them, who have been mind controlled with Dark Magic. (Stage 21:vs Peach,Palutena:playable characters:Mario,Magnus,Kirby,Geno) The team revives Palutena and Peach. (Stage 22:Battleship:Playable characters:Mario,Peach,Kirby,Magnus,Palutena,Geno)
Samus is in a factory when she sees Krystal being revived by Gannondorf through dark magic. standing at attention next to him is a dark Zelda. The Layton Mobile pulled over beside her. (Stage 23:vs Krystal,Zelda: Samus,Donkey Kong,Diddy Kong,Fox,Toon Link,Lucas,Toad,Pit,Marth,Meta Knight,Steve,Proffesor Layton) Krystal and Zelda are revived, and they fight beast gannon (Boss 3:Beast Ganon:playable characters:Samus,Fox,Krystal,Donkey kong, diddy kong,Zelda,Toon Link,Lucas,Toad,Pit,Marth,Meta knight, Steve, Proffesor Layton) they split up into 2 groups. Krystal,Fox,Pit,Meta Knight,Steve,Marth, and Toon link in one and Samus,Zelda,Proffesor Layton, Lucas, Toad, DK, and diddy in another.
Paper Mario is slipping through a crowd in a boxing arena (stage 24: boxing arena:playable characters: Paper Mario) He sees many boxers. İn the ring is Lil Mac Beating up an unnamed boxer. After he beats the boxer, he sees King K Rool challenging him. (stage 25:vs King K Rool:Playable Characters:Lil Mac) Lil Mac wins, but King K Rool tries to trash the arena. Lil Mac and Paper Mario team up to escape. (Stage 26:race to the finish: playable characters:Lil Mac,Paper Mario)
In a mushy swamp, Barry is seen, shooting up zombies (Stage 27:swamp:playable characters:Barry) After the zombie horde is defeated,he sees a figure in the distance, that figure is Link. Link and Barry team up to escape the swamp (Stage 28:Swamp:playable characters:Link,Barry)
Mario,Magnus,Peach,Kirby,Geno,and Palutena see more battleships in the distance. Fighting them off is a strange life form. He reveals himself as Bomberman and helps the heroes. (stage 29:Sky escape:Playable characters:Mario, Kirby,Peach,Magnus,Palutena,Geno,Bomberman)
Proffesor Layton and his team confront Gannondorf,Bowser, and Dark Matter in a cave. However, Gannondorf uses his dark magic to take over Samus and Zelda. The other 5 escape. (stage 30: cave:playable characters:Proffesor Layton,DK,Diddy,Toad,Lucas)
Ness is fighting off porky to defend his village. (Boss 4:Porky:Playable Characters: Ness) Ness finds Lil Mac and Paper Mario.
Link and Barry escape the swamp to find a mystic castle. Fighting off waves of monsters in the castle are Ike and Micaiah. Link and Barry decide to help. (Stage 31:Castle siege:playable characters:Link,Ike,Micaiah,Barry)
In a dark room, Luigi is being hired by someone to investigate a haunted graveyard. The man looks directly at luigi, revealing to be King DeDeDe.
Meta Knight,Fox,Krystal,Pit, Marth, Toon Link, and Steve see the Halberd fighting of battleships. They see it is being piloted by Falco. Meta Knight and Pit fly up to the halberd while fox,krystal,steve,marth, and toon link take down the monsters down there. (Stage 32:Defeat 45 enemies:playable characters:Fox,Krystal,Steve,Marth,Toon Link)
Luigi is slowly walking through the haunted graveyard. (Stage 33:Haunted Graveyard:Playable Characters: Luigi) Walking through the graveyard he sees Bandana Dee. They decide to team up. (Stage 34:Haunted Graveyard: Playable Characters:Luigi,Bandana dee)
Ness, Lil Mac, and Paper Mario are fighting hordes of koopas and other enemies when they see Fox and his team fighting Giga Bowser, they decided to help. (Boss 5:Giga Bowser:playable characters:Lil Mac,Paper Mario,Fox, Marth,Toon Link,Krystal,Steve,Ness) they see Luigi and bandana dee running towards them. Bowser shrinks down and escapes.
The story switches to Falco,Meta Knight, and Pit aboard the Halberd. they see Link,Barry,Ike, and Micaiah escaping the castle, which has become rubble. They fly over and land next to them. (stage 34:fields:Playable Characters:Link,Pit,Meta Knight,Ike,Micaiah,Falco,Barry)
Lloyd Irving is patrolling when he sees Dark Zelda and Samus. (Stage 35: Vs Zelda,Samus:Playable Characters:Lloyd) Lloyd frees them and they see Lil Mac,Paper Mario,Fox,Marth,Toon Link, samus, Krystal,Steve,Luigi,Ness and bandana Dee fighting enemies.
Lloyd, Zelda, Samus, Lil Mac, Paper Mario, Fox, Marth, Toon Link, Krystal, Steve, Luigi, Ness, and Waddle Dee all see a strange portal in the ground. suddenly, Endermen come from the ground and wreck havoc on the land. (Stage 36: Escape: playable characters: Paper Mario,Luigi,bandana Dee,Samus,Ness,Toon Link,Zelda,Fox,Krystal, Marth,Lil Mac,Lloyd,Steve)
The halberd picks up Mario, Kirby, Peach, Palutena, Geno, Magnus, and Bomberman. Mario suggests they go to the mushroom castle.
King Dedede is in his office when he is confronted by Proffesor Layton's team. Layton sees monsters invading the office. (stage 37: Office: playable characters: Dedede, Proffesor Layton,DK,Diddy,Toad,Lucas) they see a wormhole and go through.
The heroes on the halberd land on a huge battleship. (stage 38:battleship:Playable characters:Mario,Geno,Peach, Kirby,Meta Knight,Link,Pit,Magnus,Palutena,Falco,Ike,Micaia,Barry,Bomberman) They see Bowser unleashing enemies at them. suddenly Lloyd's group comes in to help. (stage 39: defeat 80 enemies: Playable characters: Mario,Luigi,Peach,Paper Mario,Geno,Link,Zelda,Toon Link,Kirby,Meta knight,Bandana Dee,Fox,Falco,Krystal, Samus,Ness,Marth,Ike,Micaia,Pit,Magnus,Palutena,Lil Mac,Barry,Steve,Lloyd,Bomberman) The team sees a wormhole and go through.
Part 2: Heroes United
Mario and his team see Layton's team and team up. Dark Matter makes a bomb, separating everyone.
Mario, Link and Bomberman wake up in a lab, where they see Megaman fighting hostile robots. They team up. (stage 40: Wily Lab: Playable Characters: Mario,Megaman,Bomberman,Link)
Pit,Toad and Geno are woken up by Pikachu and it's trainer Ash. they are in a meadow when they are ambushed by a fleet of arwings, led by Wolf. (stage 41: Vs Wolf: Playable Characters: Pit, Toad, Geno, Pikachu, Ash) They are rescued by Falco, Lil Mac and Toon Link.
Kirby and Lucas enter a dark castle, where they see Villager tied up. They rescue him but are trapped inside. Captain Falcon punches through the castle and sets them free.
All the villains are at a sort of round table. Bowser,Gannondorf,Wario,Wolf,Bowser Jr.,Dark Matter,Claus, and King K Rool all are discussing their plan. DM calls upon his master, Zero-2, to aid them.
Pit,Toad,Geno,Ash,Pikachu,Falco,Lil Mac and Toon Link find Barry and Bandana Dee fighting enemies. The enemies keep gaining strength when Mario,Link,Bomberman, and Megaman bust in. Suddenly, The villains appear in the koopa klown car, and they summon Goomboss. (Boss 6: Goomboss: Playable Characters: Mario,Toad, Geno,Link,Toon Link,Ash,Pikachu,Pit,Lil Mac,Bandana Dee,Falco,Megaman,Barry,Bomberman) Kirby,Lucas, Villager, and Captain Falcon watch, along with Paper Mario, Meta Knight and Lloyd.