On the outskirts of Metropolis Zone, the Freedom Fighters are on the trail of a new Badnik. Sonic is surprised to find the absurd and colourful Mr. Blobnik when he was expecting something deadly. The hedgehog begins to fight Mr Blobnik without putting much effort into it, merely toying with the robot. Meanwhile in Citadel Robotnik, Grimer and Robotnik are monitoring the battle, before the Pirate Omni-Viewer appears, bringing a Metallix who takes Grimer hostage, leading Robotnik to realise the Brotherhood have gone rogue. Back on the city's outskirts, Sonic has lost patience with Mr Blobnik's idiocy, while Grimer, in the Brotherhood's clutches in the Special Zone, learns what the Metallixes have planned: Taking control of the Miracle Planet, and they need Grimer's help. Sonic's vortex meanwhile rips Mr Blobnik apart, but the hedgehog quickly finds himself trapped in a bubble. Mr Blobnik's head, still active, grabs the bubble with its attached claws and takes Sonic to Citadel Robotnik, where he is surprised to learn that Robotnik actually plans to let him go. They must join forces, or Mobius will belong to the Brotherhood of Metallix.
Sonic remembers Metallix Mark 2 mentioning a Brotherhood, and is worried about how many there could be, but he has no intention of going to the Special Zone to rescue Grimer. The hedgehog's opinion is swayed when Robotnik tells him that Grimer created the Metallixes and could make them unstoppable. With all other entrances to the Special Zone sealed off, the only way in is a Star Post, which only Sonic can use. He reaches the Egg Fortress and begins to search it, using the same entrance Knuckles and the Chaotix Crew used. After searching more than half the fortress and finding nothing, he comes across the Emperor Metallix, Grimer and two standard Metallixes. The Emperor takes the completed Alpha Device and begins to depart through the Pirate Omni-Viewer. Sonic leaps into battle and seizes the Device, but is rapidly attacked by the other two Metallixes. He takes one out using it as a shield against the other's death ray, and decapitates the last one with the Alpha Device, but is ordered by the Emperor to give him the Device, under threat of Grimer being killed. Sonic is skeptical of helping Grimer, but lacking the Metallixes' merciless nature, he is forced to surrender the Device, at which point the Emperor departs for the Miracle Planet. Sonic is fully prepared to go after them, but Grimer insists that the Brotherhood have already won.
Back on Mobius, Sonic has mustered the other Freedom Fighters (minus Tails) and they are already walking the chain to the Miracle Planet. He has given Robotnik access to their channel through the Kintobor Computer, as part of their temporary truce, but wasn't prepared to take Grimer with them, despite the scientist's knowledge, not wanting anyone snooping around the Freedom Fighters' operation. Upon the planet's surface, the Brotherhood are siphoning their power to the Alpha Device, planning to reshape the Miracle Planet to release its power once the Device is fully charged. The approaching Freedom Fighters are detected, but Sonic, having had a month to explore the planet and hide from Amy, leads the heroes into a series of underground tunnels. The Emperor sends one Metallix after them, and it is soon launching an attack on the heroes. Johnny makes a brave stand to protect his friends, but is downed, his staff snapped in two with ease by the Metallix. Sonic re-enters the battle and stuns the robot, giving Amy a chance to fire at its weak spot: its neck. The Metallix is downed, and while the Freedom Fighters aren't sure how to deal with the rest of the Brotherhood, Sonic already has a plan.... Back on the surface, the Alpha Device is fully charged, and the Emperor rams it into the planet's soil, at which point it begins to twist the landscape.
As the planet's greenery begins to be replaced with metal, a Metallix arrives, having captured Sonic and the others. The Emperor brushes off Sonic's defiance, and gloats endlessly about the Brotherhood's plans, before noticing something is wrong: Porker is absent, and the Metallix which brought the Freedom Fighters before the Brotherhood is repeating itself. Sonic grabs Amy and Johnny and retreats, giving the hidden Porker the order. With a push of a button on a small remote control, Porker gives the remote controlled Metallix the order to blow itself up in a massive explosion, taking out most of the assembled army. The Freedom Fighters congratulate the modest Porker on a stunning redesign job, but their job isn't done yet. The Alpha Device is still active and still redesigning the planet, and the Freedom Fighters can't just pull it out of the ground. The machine is booby trapped, and if it explodes, the entire Miracle Planet will go with it. Some time later, Porker has reprogrammed the Alpha Device to discharge all the stored-up energy, but the heroes' view of Mobius is becoming faint; an indicator that the Miracle Planet is beginning to disappear again. Sonic plans to return next month to make sure all is well, but as the Freedom Fighters leave, Porker notices a cause for alarm: The Metallix Emperor is still active and reactivates the Alpha Device before shutting down, having taken too much damage. Porker returns to the fast-fading Miracle Planet to undo the damage, but the planet disappears completely before he can rejoin his friends or before Sonic can rescue him. Sonic feels that they still haven't seen the last of the Brotherhood of Metallix, and there's now a whole month to go until they'll know if Porker is safe.
- This is the first instance of the Kintobor Computer operating from the laptop.
- Tails is missing from the Freedom Fighters' mission to the Miracle Planet due to being called back to the Nameless Zone, with Knuckles in tow, for The Revenge of Trogg, which ran alongside this story.