The series begins with the heroes chilling at Mario's house until they hear thunder coming from outside. Everyone jumps from their position and wonders what's going on. They all look out the window and see a storm of lighning and thunder. Everyone then decides to go outside. Luigi decides not to as Mario pulls him out. As everyone's walking, lighning almost strikes them. Shadow comments that he actually hates the storm. Sonic then says that that's a first. The heroes then get struck by lightning and then get transported to New Yoshi's Island where Chief Yoshi explains to them what's going on. Everyone is surprised and decide to go to Toad Town to tell Princess Peach.
Meanwhile, Ganondorf arrives and immediately grows power hungry for the 7 Chaos Emeralds. He then quickly finds a Chaos Emerald and begins his hunt. The heroes luckily get a ride from Professor E. Gadd when he came to check up on the island. They then get to Toad Town and Professor E. Gadd decides to check the place out on why it is abandoned. A Toad comes out and tells Mario and co. that they are all hiding because of a terror that arrived at the town moments before they arrived. A mysterious fox reveals his name to be Fox McCloud along with Falco Lombardi with Froggy and Donkey. Sonic then comments on that is pretty weird as Shadow grows annoyed of the circus show. Donkey then mocks Shadow saying he should be honored to fight elites. Shadow then gets so mad that he kicks Donkey into the woods. Star Fox then turns to Shadow as Shadow laughs and asks does anyone want to be next. Everyone quickly dashes into the woods to prepare to brawl.
Once in the woods, Mario and co. then fight team Star Fox. Mario fights Fox, Luigi fights Falco, Sonic & Yoshi fight Froggy, and Shadow fights Donkey. Mario and Fox seemed tied until Fox used his Extreme Speed to kick him to a tree. There, Fox punched Mario up and then drop kicked him down. Mario gets up and immediately uses the Fire Flower. Fire Mario then punches Fox. Luigi and Falco go at it until Falco uses his Extreme Speed and tries to shoot Luigi. Luigi then tricks Falco and uses his hammer and smashes him to a tree where Luigi kicked him up and then threw the hammer at him. Sonic and Yoshi can't seem to hit Froggy until they trick him and start to pound him. Froggy then hits them both but they both then counter and hit him in a tree where both stand to attack on both sides.
Shadow then dodges all of Donkey's attacks and beats him up. Shadow then knocks him unconscience. Shadow then takes pleasure in beating him while he fainted. Mario still fights Fox and uses his Kamehamehoo. Fox then gets up only for Mario to smash him down and then kick him up for another Kamehamehoo. Fox gets up and then stares at Mario. Shadow then kicks Donkey all the way to where Mario and Fox are. Luigi then kicks Falco and then repeatidly punches him to Fox. There they both decide to power up. Mario and Shadow then gasp and are nearly blown away by the tremendous power. Luigi just gazes at the power. Sonic and Yoshi just have their mouths hanging down in fear. Fox anf Falco then tell the heroes to prepare themselves, because the real fight is about to start.