Mario & Peach are invited to the tournament by Zelda where Mario is selected to face Kirby. After Mario wins,They were interrupted by the Halberd. It drops the shadow bugs,which form into Primids. Peach & Zelda helped Mario & Kirby fought them off until the Ancient Minister drops the Subspace Bomb that are activated by the R.O.B.s. Mario gets thrown off to the sky by Bugzzy while trying to deactivate it. Kirby transforms into Sword Kirby & kills Bugzzy,but Peach gets captured by Wario. Kirby & Zelda fled on the Warp Star as the bomb detonates,sucking the Stadium into Subspace.
In the clouds,Mario was found by Pit,who was watching him & Kirby fight & sent by Palutena to stop the invasion. In the Jungle,Donkey Kong & Diddy Kong pursues the Banana Thieves,but are ambushed by Bowser & King Rool . DK forces Diddy to fled before getting captured. Diddy found an Arwing that was shot down while attacking the Halberd. He was later attacked by Necky,but Fox manage to save him before they confronted Bowser & Rool. After defeating them,They realize that the Bowser they fought was a Shadow & the two escapes.
Lucas wonders around in the town where he is attacked by Pokey Minch. Ness came to his aid to defeat Minch,But gets captured by Wario. Lucas fled & met Green,who was seperated from Red since he was captured. At the Castle,Marth witness the Subspace & fought against the Army with Meta Knight & Ike's help. Meanwhile,Wario's vehicle gets hijacked by Dedede,who captured Luigi,& drove away the captured Peach & Ness. Kirby saw him driving & pursues him as Zelda gets captured by Bowser & the Shadow Bugs took form of her. She gets defeated by Mario & Pit,but are attacked by Link & Yoshi,who pursues the Halberd. After Link & Yoshi are defeated,They are nearly captured by Dedede,but are saved by Kirby and they pursue him to his castle. Ganondorf send Bowser to Dedede's location and was greeted by Master Hand. After breaching in,Bowser captures Peach and the castle is sucked into Subspace.
Lucas & Green arrives at the ruins where they defeat Wario and captures Vulpix & Kangaskhan. Marth,Ike,& Meta Knight pursues the tank who transforms into a robot,Galeom,who fled and went through the ruins where He was defeated by Lucas and Green. He later self-destructs,sucking the ruins and Wario into subspace,but Meta Knight helped Lucas & Green escapes. At the float island,Samus infiltrates inside where she found Red. They are attacked by Ridley,but they quickly defeat him. Olimar & the Pikmin are attacked by Black Bison,but Captain Falcon defeats him. Fox & Diddy are attacked by King Rool,but gets defeated by Falco,who helped Diddy freed DK. They went inside with Captain Falcon & Olimar.
Meta Knight went on the top of the mountain where he & the Ice Climbers are confronted by Lucario. The Halberd attacks,knocking the Ice Climbers down the slope where Mario,Link,Kirby,Pit,& Yoshi helped the heroes out. Meta Knight & Lucario soon discovered Solid Snake,who stowaways in the ship,and freed the Princesses. They later knocked out the Five & Watches,who form into Duon. With Fox & Falco's help,the Heroes defeats Duo,who purifies back into the real Game & Watch. Samus,Red,DK,Diddy,Falcon,& Olimar confronts The Ancient Minister,but he refuses to fight and reveals that he was forced to by Master Hand. Ganondorf is aware of his betrayal & order the R.O.B.s to burn him,but the Ancient Minister reveals to be a R.O.B. and helps them fight off the enemies. They quickly escape as the island is sucked into Subspace.
They gather the Heroes & went inside Subspace where Ganondorf betrays Bowser & planned to betray Master Hand as well,but realizes that he was controlled by Tabuu,a true enemy. The Heroes appear and get turned into Trophies along with Ganondorf. They are both saved by Dedede,Ness,& Luigi. Tabuu has Master Hand & Crazy Hand to attack the Fighters,but are stopped by Sonic the Hedgehog. Tabuu then fuses the Hands into a Golem.
After the Heroes defeated the two villains gets defeated,The Golem turned on Tabuu and self-destruct to destroy him. With Tabuu destroyed,The Subspace disappears. As the Heroes looked at the sunset,Ganondorf disappears & Bowser fled in the Clown Car. Unbeknownst to them,The Golem's hand that was severed forms into slime and slithers away.