the portal that lucas and toon link entered is still open. From the portal mewtwo emerges. Mewtwo has a look of anger on his face. this anger destroys the conjured portal. He wants revenge on master hand for leaving him behind. He sends out a telepathic message to ganondorf and bowser and tells them to gather the villains of the world and meet him at ganondorf's castle bowser brings bowser jr eggman wario and zero. Ganondorf brings andross ridley porky black shadow and metal sonic. Mewtwo tells them the plan to overthrow master hand and control the universe. Ganondorf explains that overthrowing master hand would require an item that could absorb his energy. zero says the star rod could absorb his power and goes to retrieve it. Mewtwo demands and army to invade the area's of the smash world and ganondorf offers that we kidnap mr game & watch as he contains shadow bugs that can be used to duplicate minions and make an endless army. Wario is sent out to get game and watch. Mewtwo tells andross and eggman to build a portal to master hand. And andross says that would require a massive power source. Eggman says the chaos emeralds could power the portal but sonic has them. Mewtwo sends out eggman and bowser jr to retrieve the emeralds.
At the fountain of dreams. King dedede is checking up on the fountain to see if is alright. Suddenly the skies get dark and zero appears to steal the star rod. King dedede attempts to fight zero but is possessed by a dark matter. Zero and dedede steal the star rod and return to mewtwo..
Meanwhile game & watch is playing around when wario appears to fight him game & watch attacks wario but wario defeats game & watch and turns him into a trophy. Wario returns to mewtwo
meanwhile also sonic tails and knuckles are racing when their ambushed by eggman and bowser jr who is in the guise of shadow mario. Sonic tails and knuckles think shadow mario is the real mario. Shadow mario blasts tails with a trophy gun and turns tails into a trophy. He blasts at knuckles but knuckles digs underground Sonic angered that mario would hurt his best friend turns into super sonic And charges for shadow mario. Shadow mario blasts sonic with the trophy gun but instead of turning sonic into a trophy an explosion occurs that scatters the chaos emeralds. Shadow mario attempts another shot but knuckles emerges from underground and destroys the gun. Eggman angered by this grabs the tails trophy. Shadow mario opens a paint portal and eggman and shadow mario jump in taking the tails trophy with them. Sonic and knuckles know that they must get both tails and the chaos emeralds back.
at ganon's castle wario returns with the game & watch trophy and andross proceeds to extract shadow bugs. Zero and Dedede enter ganondorf's castle with the star rod. Zero tells mewtwo that a dark matter is possesing Dedede as he hands mewtwo the star rod. Bowser jr and eggman emerge from the paint portal. Mewtwo asks where the emeralds are and eggman says they got scattered but they brought mewtwo a trophy of tails. Mewtwo then decides to turn all of the heroes into trophies so they can't stop his plan. He has dedede zero and black shadow go steal the halberd to transport the shadow bugs army around. Mewtwo put andross and eggman to work on the portal and has ganondorf produce more shadow bugs. Mewtwo send bowser bowser jr metal sonic ridley porky and wario to turn the fighters into trophies and find the chaos emeralds bring them to him bowser bowser jr and metal sonic go after mario. Wario goes off on his own and ridley and porky go after samus and ness respectively
at that time meta knight and captain falcon were having a match in the halberd hanger. When out of nowhere black shadow appeared with an army of waddle dee's and waddle doo's and attacked the two. Captain falcon and meta knight defeat the enemies but not before dedede and zero steal the halberd and black shadow leaps aboard. The halberd flies away And meta knight and captain falcon pursue them.