After having a severe lost to the Mecha Sonic Bros. Mario drags The heroes back to his house. THey all wake up to find out that they lost to the Mecha Sonic Bros. Shadow then gets mad and says that he will kill them next time. Professor E. Gadd comes and shows the heroes a Emerald Emerald Finder. Mario takes it and Sonic asks what he means. Shadow then explains it. Princess Peach checks up on Yoshi as the gang gets ready to head out to New Yoshi's Island. The heroes all go outside except when Luigi are outside when Peach calls him and gives him a 1-Up Mushroom. The heroes then go to New Yoshi's Island. Peach checks up on Yoshi again, only to find out that he's gone missing. The gang gets to New Yoshi's Island in no time and spot a Chaos Emerald.
Professor E. Gadd goes retrieve it but gets stuck in a tree because of Blue Shell Koopas. Red Shell and Green Shell Koopas then appear as well. Then a giant Yellow Shell Koopa appears. Shadow gets the fake Chaos Emerald and beats up a Red Shell Koopa. Luigi and Sonic then team up and fights the Koopas witht heir hammer ball technique. Mario handles two at a time and easily takes over the fight against them. Mario continues to beat them up and soon more are sent to kill Mario. Shadow then takes down four of them and watches the others. Luigi hits three in a row with his hammer and Sonic then rolls over all of them. The giant Koopa then attacks and kicks Luigi to a tree. It then fights Mario as Mario struggles to dodge its every move until it hits him back. A Koopa then strikes Sonic. Shadow watches in humor. A Native Yoshi and Yoshi saves Mario. Professor E. Gadd is let down by Thundefoot.
Chief Yoshi welcomes the heroes back to their island but tells the bad news. They said that many people of a range of 9 are terrorizing their island. They then show that the Native Yoshi's are working for someone. Mario and co. then breaks the anklets and cuffs off the Yoshi's. Chief Yoshi thanks them but then a giant shadow casts upon the heroes. It was the Blade. Five robots swooped down and called themselves the Axem Rangers X. They all then remember Mario. The Koopa Bros. then comes and said that Kammy & Kamek resurrected them. As a new terror omens, the Mecha Sonic Bros. appear and the heroes are anxious to retrieve the radar and the Emerald. They all then get ready to enter a four way battle. Chief Yoshi tells the heroes to be careful and Professor E. Gadd tells him that maybe they should step back. All the teams then fight as each from one team fighst others.
Sonic fights Yellow Koopa, Semi-Mecha Sonic #2 and Axem Yellow. He easily beats up the first two but Axem Yellow quickly hits him. Luigi fights Semi-Mecha Sonic #4, Green Koopa and Axem Pink. Luigi gets beat up by all his opponents but quickly gets them back with his hammer. Shadow fights Axem Black, Black Koopa and Semi-Mecha Sonic #3. Yoshi only fights Axem Green as he quickly beats Axem Green up. Mario, Red Koopa, Axem Red, and Semi-Mecha Sonic #1 all duel it out as each hurt one another back and forth. Mario then punches Semi-Mecha Sonic #1 as Red Koopa teams up with him only for it to backfire and Axem Red slashes all of them. Shadow easily beats up his opponents and uses his Chaos Blast on Semi-Mecha Sonic and obliterates it into dust. Axem Black gets shocked by this as Shadow kicks him to a wall. Mario and Semi-Mecha Sonic #1 keep fighting until Red Koopa kicks them both. Red Koopa then duels with Axem Red and beats him up. Mario then beats up Red Koopa and then throws him to Semi-Mecha Sonic #1. Axem Red then kicks Mario and uses his Bladege Sychronize.
Mario falls but quickly gets up but is beat up by all the opponents he is facing. Sonic tricks his opponents but gets Axem Yellow to destroy Semi-Mecha Sonic #2. Sonic then kicks Yellow Koopa and punches Axem Yellow up. Luigi and Axem Pink goes at it until Luigi wins but Green Koopa then keeps beating on Luigi until Semi-Mecha Sonic #4 uses his Cyclon Demolisher and defeats Green Koopa. Axem Pink then punches Luigi and battles against Semi-Mecha Sonic #4. Semi-Mecha Sonic #4 knocks Axem Pink away but is attacked by Luigi and Green Koopa. Green Koopa then is kicked to Axem Pink where she strikes him 405 times in a row.
Mario then fights Semi-Mecha Sonic #1 alone but gets beat by his speed and soon he and Red Koopa fight until Axem Red double kicks both of them. Shadow then uses his Chaos Spear on Axem Black and Black Koopa. Black Koopa tries to fight back but keeps getting hurt.Yoshi and Axem Green keep going at it until Axem Green uses his blade and Yoshi falls. Yoshi gets up, turns into an egg, and then rolls and bashes Axem Green. He then nearly killed Axem Green with his eggs and then slaming his body on his. As this fight is happening, Wario and Waluigi are taveling to the same island. Ganondorf then heads for the next Chaos Emerald and finds his fourth one.