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Prior to the game, Bowser ambushed Peach's castle, but was fended off by some of the Nintendo Heroes.(The Mario Bros,Kirby,Link,Megaman)
The game starts with Peach hosting an awards ceremony. Mario,Luigi,Link,Kirby and Megaman walk up to the stage and are given gold medals. However, Bowser comes in his koopa airship, with Bass and Bowser Jr. at his side, and abducts Peach. Megaman tells the others to go after Bowser while he fights Bass. So the adventure begins: Mario,Luigi,Kirby and Link chase after Bowser in his airship.
In skyworld, minions are attacking Palutena's castle. Pit and Magnus fend them off, but a few koopas take Palutena into their airship.Magnus tries to stop them, but he is turned into a trophy and taken away by paratroopas. Pit, forced to fend for himself, flies off.
Sonic and Blaze are fighting off badniks in the area, when Bowser Jr. attacks them. Bowser Jr. turns Sonic and Blaze into trophies, and Blaze with him to the airship.
Blaze is reawakened, tied up, where she sees a man in a black hoodie and black pants, where the only things visible on his face are bright yellow eyes and a red dragon tatoo around his left eye. The man introduces himself as Nexus, the Dark Dragon, and claims he is bringing Blaze and the other girls to his airship for bait. He then laughes evilly before the screen fades to black.
Zelda is in Hyrule Temple when she is ambushed by minions and taken away. Toon Link and Toon Zelda see this, and the two set out after the airship.
Pit is searching for help when he sees the trashed area where the assembly was. He sees Bass huffing, and Megaman as a trophy (implying that Bass won the battle) Pit knocks Bass out in the head with his sword, turning Bass into a trophy. Pit then revives Megaman and the two team up.
Zelda wakes up in a room, where she sees Peach's trophy, surrounded by minions and traps. She gets through the traps, but the moment she is about to revive Peach, Zelda triggers a last resort trap and becomes a trophy herself.
Sonic is revived by his best friends, Knuckles and Tails. The trio decide to go find Blaze. Tails goes to get the Tornado, but he is turned into a trophy by King Dedede, who escapes with him in the Tornado.
Steve finds Enderman harassing villagers, and the two fight. The two see a portal and, despite Steve's advice, Enderman recklessly goes in.
Spyro is having trouble fighting off minions, when Rosalina comes and helps him. Gannondorf appears and grabs Rosalina.Spyro tries to help her, but Gannondorf sends Ghirahim to distract him, but Toon Link and Toon Zelda come to help him. Ghirahim is defeated and turned into a trophy, but it is too late. Gannondorf escaped with Rosalina.
Mario and his gang fight through minions to get to King Dedede's castle. After fighting through minions, they make it to the castle. King Dedede turns Luigi into a trophy and locks him up as the fight begins. The team defeat Dedede but can't revive Luigi.The heroes escape before the minions find them.
Enderman ends up in Nexus' lair, but Nexus turns Enderman into a trophy. A cutscene is shown where he locks the trophy up with the trophies of Peach,Zelda,Magnus,Luigi and Tails.
Palutena is thrown in the main room by Bowser. Blaze breaks free with her flames, but Bowser transforms her into a trophy.
Donkey Kong is after King K Rool, who has captured Diddy in his lair. By the time Donkey Kong gets to the lair, King K Rool turns him into a trophy. He then prepares to turn Diddy into a trophy aswell but Isaac blasts him and frees Diddy. King K Rool kicks DK's trophy into a pit, and then is picked up by the airship. Isaac and Diddy begin their quest.
As DK's trophy falls into the endless abyss, it is rescued by a passing arwing.
Sonic and Knuckles continue to chase after the airship.The two see Toon Link and Toon Zelda riding Spyro, who is shooting the airship with his fire breath. After one shot, the airship spills out the trophies of Tails,Luigi,Magnus, and Enderman.The five revive the trophies and decide to split up to find more help. Sonic,Knuckles,Tails,Spyro and Luigi in one group and Toon Link,Toon Zelda, Enderman and Magnus in the other.
Megaman and Pit infiltrate the airship, where they see Nexus, Palutena and Rosalina in chains, and Blaze's trophy. The two revive Blaze but Nexus creates a wall between the three and him and the girls.
Mario,Link and Kirby enter a labaratory. They see Zero Suit Samus, unconscious, and Ridley, who roars at the heroes. Right before the fight begins, an electric jolt goes through Ridley. Pikachu appears to help the heroes defeat Ridley. After the heroes defeat Ridley, Zero Suit Samus wakes up, and sees what happens. The five decide to team up and look for her power suit.
Fox lands his arwing in a village and revives Donkey Kong. The two see Steve having a scuffle with an Iron Golem. Fox breaks it up as the four see an airship in the sky. The four pile into the arwing and set out.
After a level of searching through the lab, Mario and co. see Samus' suit in a pod. Zero Suit Samus tries to get it, but the pod flies away, with the suit in it. Mario and the gang get on Kirby's warp star follow it.
Yoshi is sleeping when he hears a strange noise. Yoshi gets ready for battle, when he sees Geno fighting minions. Yoshi decides to help Geno fight the minions, who are coming from the airship. Yoshi and Geno go after the airship.
Peach wakes up with Zelda,Palutena and Rosalina in a dark room. All four of them have a device on their wrist, preventing them from using their powers.
Jigglypuff is roaming through the region when Gannondorf appears and attacks her.After the battle, Gannondorf is about to strike when he is attacked by a yoshi egg. However, the spots on the egg are more yellowish then green, and Mewshi emerges from the egg. Gannondorf teleports away.
Nexus summons the trophies of the defeated villains (Ghirahim,Bass,Ridley, Dedede) and revives them.
Mario and the crew are chasing after the pod until it reaches the airship. The crew get in the airship, as they fight clones of the suit. After the clones are defeated, Samus gets in her suit as the team searches for the princesses.
Diddy and Isaac are in a forest when kremlings attack them. Diddy and Isaac are turned into trophies after the ambush. Klonoa sees the trophies being taken away and tries to free them. King K Rool arrives and prepares to turn him into a trophy as well, but he is stopped by Fox,DK,Steve and Iron Golem. The group teams up with Klonoa and revives Isaac and Diddy. King K Rool escapes as the battle begins.
After a while of searching, Mario,Link,Pikachu, Samus and Kirby find Nexus with Peach and Zelda in a room. The team destroy the devices around Peach and Zelda's wrists as they fight off the minions. The dialogue is as follows.
Mario: What else do you have up your sleeve, cold hearted monster?!?
Nexus: Oh I have something up my sleeve alright.
Suddenly, Rosalina and Palutena grab Peach and Zelda and lock them in another room.
Link: I am going to KILL YOU!
Link attacks Nexus, but Nexus blocks him and shoots dark energy at Link, turning him into a trophy.
Nexus: If only that were possible. Now you will all die by the power of I, NEXUS, THE DARK DRAGON!
Nexus prepares another energy beam, but Megaman,Pit and Blaze bust in and counter it.However, Nexus opens a flap in the airship floor, causing Mario,Pikachu,Kirby,Samus,Pit,Megaman and Blaze to fall out, and then closes it again.
Wario is out walking when he sees a trophy of Squirtle. He believes it's very valuable, but Ash absorbs it into his pokeball, saying it's his.Wario gets angry and is about to attack him, but they see Sonic,Knuckles,Tails,Spyro and Luigi fighting minions and decide to help.
A black figure sees seven trophies in the distance and teleports to them.
After some platforming, Toon Link and the gang find a temple and go inside. Inside they see Nexus, who creates a shockwave and turns the team into trophies.
Shadow teleports to the trophies of Mario,Pikachu,Kirby,Samus,Blaze,Megaman and Pit (Who became trophies from the fall) He lets out a grunt and refuses to revive them, but Geno and Yoshi come along and convince him. However, before they can be revived, minions come and Geno,Shadow and Yoshi defeat them. Shadow teleports away, leaving the group to fend for themselves. Geno and Yoshi revive the trophies. They see the airship and split up into two groups: Mario,Kirby,Yoshi,Megaman and Pit on the warp star and Samus,Blaze,Geno, and Pikachu in Samus' ship.
Samus' ship arrives near the airship and Samus,Geno,Blaze and Pikachu get in. They find Mewtwo and defeat him, but Nexus arrives and turns them into trophies with a shock wave.
Fox,Diddy,DK,Klonoa,Isaac,Steve and Iron Golem see the airship in the sky. DK jumps up into the airship to help the other nintendo heroes. DK jumps up into the airship and beats Nexus up, but is attacked by Ridley. After defeating Ridley, DK walks into another room.
Link, Peach, and Zelda are locked up in a room, with no means of escape, when a big hand punches through the locked door. Donkey Kong,Link,Peach and Zelda escape the room and try to find help. They look in a room and find the trophies of Samus,Geno,Pikachu, and Blaze and revive them. After some platforming, the team gets to the main room, where Nexus is waiting with a giant mech. However, right when the mech is gonna attack, Mario,Kirby, Megaman,Pit, and Yoshi bust in to help. Before the boss begins, Pit looks at Mario,Kirby,Yoshi and Link, and utters "Just like old times" followed by a flashback of Mario,Pit,Link,Yoshi and Kirby beating up primids.
After the boss' defeat, the airship explodes, causing the gang to blast in all directions.