Ganondorf goes off looking for the Chaos Emeralds he lost. The heroes now have 4 Chaos Emeralds, and Semi-Mecha Sonic owns two. Sonic asks if Mario got the Emerald Radar, to which he says yes. Shadow then sighs of relieve. Yoshi and Professor E. Gadd carries Luigi here after he fell in the water again. They then bid Professor E. Gadd farewell as he leaves. Mario and co. then finally sets out to find the remaining Chaos Emeralds and get the ones the villains have.
Bowser and Dr. Eggman are then introduced and show Mecha Mario, the ultimate weapon. Mario and co. goes to back to New Yoshi's Island and discovers hidden connections. Sonic and Shadow then reference this to the Chaos Emeralds. Chief Yoshi then taes the Emeralds and their Key Elements are revealed. Mario, Sonic, Luigi, and Shadow all take the Key Elements and place it inside of them. Luigi shares some of his with Yoshi as well as the other heroes. Now they can see things that is beyond Supernatural and Mobius. Meanwhile, Semi-Mecha Sonic makes a recreation of Mobius through a portal with the power of the Chaos Emeralds he possesses. Ganondorf hot on his trail follows him through the portal and Wario and Waluigi both get lost at sea. The heroes then go and seems to meet up with Stuffwell.
Stuffwell then shows the heroes to Goombella and Dr. Frankley. They then quickly go and they see a portal. They all go in it but Luigi hesitated until Mario pulled him in. Yoshi then carried Luigi as the heroes and Stuffwell venture through a wormhole. They then enter another realm what seems to be Mobius. Sonic and Shadow then smile and thank Mario and Luigi. They then go check it out as they see in the distance Semi-Mecha Sonic fighting off Ganondorf. Both keep hurting one another and can't seem to stop the other. Once Sonic tries to help Semi-Mecha Sonic, the latter turns against Sonic and steals one of his Chaos Emeralds. Sonic then uses another Emerald and Ganondorf goes after both of them. The two then work together and fight Ganondorf. Ganondorf quickly uses his Cyclone Buster and Sonic and Semi-Mecha Sonic go flying. The other heroes prepare to fight as the two Sonics fight Ganondorf and overwhelms him with their Blue Tornado. Ganondorf gets up and laughs. Stuffwell then tells Sonic to watch out and not to trust any of the villians. Semi-Mecha Sonic then attacks Ganondorf but Sonic attacks him first but gets hit to a boulder.
He then watches in agony as Semi-Mecha Sonic is destroyed by the Cyclone Buster. Sonic and the other heroes get enraged as Ganondorf gets 3 Chaos Emeralds. The heroes and Ganondorf then prepare to fight around the recreation of Mobius. Dr. Frankley and Goombella then watch with Stuffwell as the heroes fight. However, Ganondorf easily beats them all up until they all work together and beats on Ganondorf. Afterwards, they hid from Ganondorf as he steals a fourth Chaos Emerald and transforms into Morph. When the heroes are found, they get beat up in the order: Yoshi, Shadow Luigi, Sonic, and then Mario. However, Mario uses a Cape Feather at the last second and ties with Morph until Morph powers up. Morph then thrashes Cape Mario. Luigi enraged to his breaking point, beats up Morph and does a combo with Sonic, then Shadow, and finally Yoshi. Mario then awakens and stops Morph from killing Goombella. Mario then kicks him and the five work as a team and ties with Morph. Meanwhile, Mecha Mario is being ready to be sent and kill the heroes.
The heroes get beaten again and this time hides near the portal under a tall building. Shadow then thinks of a plan and Yoshi and Luigi are used as bait. They both are chased by Morph until Yoshi and Luigi kick and punch Morph and then Sonic uses his Hurricane Kick. Mario then uses his hammer and smashes him down as Shadow uses his Chaos Blast x2 and nearly kills Morph, powering him down. The heroes then escape the fake Mobius with their lives and Ganondorf leaves before it explodes. Ganondorf reveals to have gotten four Chaos Emeralds while the heroes have two. He then leaves and promises to return later.