Dr Robotnik has been imprisoned by the Freedom Fighters, and it's Porker's turn to interrogate him. Easily seeing the hapless pig's fear however, Robotnik only frightens Porker even more when questioned about his new generation of Badniks. Suddenly, a tremor shakes the heroes' base, and Knuckles the Echidna bursts out from beneath Robotnik's cell to rescue the dictator. Porker calls for help from Sonic, but is grabbed by Robotnik before the hedgehog can get there. The dictator's ultimatum: the Chaos Emeralds in exchange for Porker. Before Knuckles and Robotnik leave with the Emeralds, Sonic questions the dictator as to how Knuckles found him. Robotnik reveals that he has implanted a device into Knuckles' skull, tuned to the frequency of a homing device in one of Robotnik's teeth. Sonic rushes back to the Kintobor Computer, who has already tracked Knuckles and Robotnik down, and quickly heads for the Bi-plane with Tails. They quickly catch up to Robotnik's escape vehicle, and Sonic is able to knock it out of the sky, sending it crashing into the Floating Island. When Sonic investigates the crash site, Knuckles bursts out of the wreckage and the two begin to fight again.
Sonic is able to fend Knuckles off with his sheer speed, Spin Attacks and his new forcefield. Knuckles, however, has his home's traps on his side, and activates giant stone hands to hold Sonic in place while Robotnik takes a nearby Zoom Tube to the Temple of Chaos. Faking being trapped, both to throw Robotnik and Knuckles off and display his weird sense of humour, Sonic quickly breaks free and heads for the Zoom Tube. In the temple, Knuckles laments not having the Grey Emerald to control the twelve Emeralds' power, but Robotnik has fashioned a device to act in the same way as the Grey Emerald. He merges the twelve emeralds back into six and then proceeds to absorb their power, turning on Knuckles just as Sonic and Tails arrive. Robotnik uses his new power to turn Tails into a glass statue, Sonic only just managing to catch him, but then Knuckles reveals his trump card: the Grey Emerald. The Echidna drains the Emeralds' power out of Robotnik, and teleports him back to the surface of Mobius, also returning Tails to normal. Sonic offers Knuckles a place in the Freedom Fighters, but the echidna refuses. The war against Robotnik is none of his concern, and he plans to continue waiting for his people to return from the stars. As Sonic and Tails quietly depart, leaving Knuckles to be alone, the blue blur can't help but feel that they haven't seen the last of Knuckles yet.
- The first of Robotnik's threats to Porker is known in the Message Zone's Butchery for being a rare case where nothing needs to be done to a panel to make it amusing.
- Knuckles changes colour between each part of the story, going from a pinkish-red to the red of his shoes.
- Robotnik would later use the same tactic of absorbing the Emeralds' power in Robotnik Reigns Supreme, with much more disastrous consequences, though he would still ultimately be defeated in a similar manner to this story.