The Freedom Fighters are standing on a deserted beach on the east coast of the Emerald Hill Zone in readiness. Something is coming for them: the Emerald Hill folk, home from the Floating Island in a procession of small boats. As the people return to the Zone, the Floating Island rises back into the air, and the heroes recieve a call on the laptop from Knuckles, happy that the Island is truly his again. Porker appears to let Sonic know he'll be staying on the Floating Island to help fix the ancient systems, but Sonic slams the laptop shut in disgust when Knuckles tells the hedgehog he can now retire. Nonetheless, he's worried at the idea of having nothing to do now that Robotnik has been deposed. A few days later, Sonic, naturally, has become bored, but is distracted by Tails calling for help. Tails takes Sonic to see a small Flicky, who has somehow told Tails there's danger apparent. Elsewhere, on Flickies' Island, Robotnik and Grimer have completed a number of tests on another Flicky and deemed the Flickies suitable future organic batteries. As Robotnik proclaims himself the Flickies' new master, ignoring the fact that their other captive Flicky escaped, Sonic and Tails make their way to the island in the bi-plane.
The heroes arrive on the island, where Sonic learns just how Tails can understand the Flicky, before they set off to explore, soon coming across an ancient ruin. As Sonic investigates, thinking the place deserted, they are quickly greeted by Robotnik, surrounded by new Badniks. The dictator has long wanted to investigate Flickies' Island, but had to speed up his plans after the Final Victory, as he elaborates while feeding a number of wires through a massive glowing ring. Suddenly, he pulls the wires out of the ring, with a Flicky attached. Now knowing how to catch them, he plans to use them as organic batteries for his new range of Badniks, which he sends forward. Sonic launches into battle, but oddly enough his spin attack fails, the Badniks seeming to be strengthened by the Flickies. With a little more effort put in, Sonic is able to smash the attacking Badnik, but the time it took him enabled Tails to be captured.
With Sonic unable to do much, Robotnik gloats about his future plans and orders the hedgehog into a cage. Before Sonic can move however, the ring glows with a blinding light, and out steps a massive armoured figure, declaring himself as a Prosecutor of the Drakon Empire, here to find out who discovered the secret of the Mobius Ring. Sonic takes advantage of the situation to smash the Badniks holding Tails, and prepares to attack Robotnik, ignoring the Prosecutor's order to freeze. The Prosecutor uses his weapon to increase the gravity in the room, forcing everyone but him down, and asking again who learned the Ring's secret. He elaborates that the Ring was left behind when the Drakons left Mobius, knowing that when the people of Mobius became intelligent enough to understand the Ring's technology, they would be a threat. Sonic states that Robotnik is the real threat in the room, leading the Prosecutor to seize the dictator, preparing to take him back to the Drakon Empire for interrogation. Proclaiming that Robotnik is Mobius' problem, not the Drakons', Sonic attacks the Prosecutor, damaging his armour slightly, but is downed by a shock administered by the Drakon. Tails swoops in, but is unable to stop the Prosecutor before he gets through the ring, shutting it down. As Sonic muses upon the Drakon Empire, Tails checks out a broken part of the Prosecutor's armour. Sonic recognises the face on the chipping, but can't think where he's seen it before. The heroes quickly leave, not quite sure they've seen the last of Robotnik yet....