Dr Robotnik, still with the Chaos Emerald-induced power of a God, has conjured up a new Metallix which is coming down hard on Sonic. The hedgehog continues to defy Robotnik, despite what the dictator has done to Mobius, adamant that he'll win somehow and he's been in worse spots, at which point Metallix's attacks become fiercer. Sonic is blasted into a puddle of Mega Mack, which swiftly forms into Megatox, visualised into being by Robotnik. Sonic vows to keep fighting, at which Plasma and Arnem Abacus enter the fray. Upon Sonic's mocking of Robotnik's latest addition to the battle, the dictator summons a more worthy foe from a pile of junk: Commander Brutus! Now that Sonic is outnumbered six to one, Robotnik decides to even the odds and brings back Tails. Unfortunately, Sonic is now outnumbered seven to one, as 'Tails' is revealed to be Metamorphia. Sonic fights back, blowing off his predicted demise from Robotnik, and knocks Brutus into Plasma, destroying the Trooper. Plasma's electrons are disrupted by his collision with Brutus, and as the energy tears into the other assembled villains, Sonic begins to move to safety. Unfortunately, he is caught in the ensuing blast. Sonic soon finds himself being teleported elsewhere by Robotnik. Round one is over, but the worst is yet to come.
Sonic arrives in the Special Zone, where he bumps into Vector the Crocodile. Unfortunately, he can't call the rest of Chaotix: he's just the local cleaner, and Robotnik has altered history so Chaotix never existed. The hedgehog is immediately face to face with a gargantuan Robotnik again, and is quickly walloped by Mr Fry upon insulting Robotnik. A quick glance behind reveals Lord Sidewinder and his cronies, Sidewinder referring to himself as Overlord. Without Chaotix to stop him, Sidewinder now rules over the Special Zone, but Sonic isn't about to let that stop him. However, purely because he can, Robotnik has taken away Sonic's speed and skill, and the hedgehog is left to the mercy of Fry and Bio-Hazard. Sidewinder and Lightmare watch, discussing their main objective once Sonic is dead: stealing Robotnik's power so Sidewinder can rule the entire universe. Being omniscient, Robotnik hears this, and turns Sidewinder and his group to stone. Robotnik blasts apart the rock Sonic is standing on, and the hedgehog continues to mock Robotnik for still fearing him enough to take away his power. Sonic is just glad that Knuckles isn't around to see this. Robotnik, seeing this as a challenge, returns Sonic's power and sends him to the Floating Island. Sonic's trick has worked, and he quickly seeks out Knuckles, but is surprised to find that the Echidna is once again on Robotnik's side.
As Knuckles launches into several attacks, Sonic tries another trick with Robotnik: Accusing him of turning Knuckles bad purely because while Sonic would still win somehow alone, having Knuckles on his side would make it a lot easier. Robotnik laughs it off in his arrogance, but Sonic dares Robotnik, at which point the incensed dictator turns Knuckles back to normal. Knuckles starts coming to his senses, but before Robotnik can destroy them both, Sonic requests that Knuckles have a little time to readjust. They are granted 100 seconds, and the heroes retreat to the Emerald Chamber, where their attention is diverted to the machine Robotnik used to absorb the Emeralds' power. Robotnik arrives, stating that only he knows how to use the machine, and trying to use it to take back the Emeralds' power wouldn't work. That wasn't the plan however: Knuckles has got into position, and the Echidna uses the Grey Emerald on Robotnik, draining his power away and reconfiguring the energy into its original pattern, undoing what Robotnik has done. Robotnik, his body so accustomed to being Emerald-powered, shrinks away into nothingness.
Soon, Sonic and Knuckles are walking through the Emerald Hill Zone, the damage undone and nobody remembering a thing. Sonic is depressed however: They have defeated an enemy who could kill them with a thought, but Sonic can't be the big hero today, purely because no one remembers it, bar him and Knuckles.