The Brotherhood of Metallix was an army of Metallix robots in Sonic the Comic. Intially created to create the ultimate robot duplicate of Sonic from Dr. Robotnik's old Egg Fortress in the Special Zone, the Brotherhood quickly went rogue under the leadership of their Emperor and sought to conquer Mobius through time travel. The Brotherhood remain the most popular of Sonic's adversaries in Sonic the Comic to this day. Writer Nigel Kitching has since stated that the idea of an army of robots led by an emperor was indeed borrowed from the Daleks.
Not long after their creation, the Brotherhood contributed a new model of Metallix to retrieve the Master Emerald from the Floating Island's Emerald Chamber to power Robotnik's new Death Egg. The Metallix was undoubtedly powerful, drawing power from the Master Emerald, but before he was ripped apart by Super Sonic, he spoke of the Brotherhood, indicating that the robots had already gone rogue.
A short time later, the Brotherhood captured the Omni Viewer in order to create a copy of it for their own means. Knuckles the Echidna and the Chaotix Crew, guardians of the Special Zone tracked the stolen Omni Viewer to the Egg Fortress, but one member of Chaotix, Nack the Weasel betrayed the team, telling the Brotherhood how to obtain the Omni Viewer, and leading the heroes right into the Emperor's clutches, all in the name of money. The Emperor then ordered Nack be killed, having served his purpose, and the weasel just barely escaped death, not taking the full force of the attacking Metallix drone's death ray. Knuckles however was able to activate Nack's disruptor cannon and shut down every Metallix in the Fortress, including the Emperor, enabling the heroes to retrieve Omni and leave. They reactivated a short time later thanks to their back-up power supply, and then captured their creator Grimer Wormtongue, via their pirate Omni-Viewer, to force him to build them an Alpha Device. This device would enable them to terraform the Miracle Planet, and while Sonic tried to stop them in the Special Zone, he couldn't let the Emperor kill Grimer and was forced to return the device to them. Sonic later led his teammates onto the Miracle Planet, where the Brotherhood were already beginning to terraform the planet into a metal state. The Brotherhood were mostly destroyed by a Metallix drone Porker Lewis had converted into a walking bomb. The Emperor remained active however and restarted the planet's terraforming process, which led Porker to return to the planet to undo the damage again. The planet faded away before he could finish or Sonic could rescue him, leaving the Freedom Fighters with a whole month to wait until they knew if Porker's mission had been successful.
When the Miracle Planet reappeared, now fully mechanized and in the shape of a Metallix head, Sonic and the newly arrived Chaotix Crew battled a Porker-themed Metallix on the planet's chain and were able to defeat it. In the time they spent fighting however, they had not noticed what was happening behind them. The Brotherhood had used their pirate Omni Viewer to alter time, turning Mobius into a twisted metallic nightmare: Planet Metallix. Sonic, Porker and Chaotix soon came face to face with the Underground, the few remaining people of Mobius who were still organic, led by Sonic's old friend Professor Ovi Kintobor. The Metallixes had removed the rotten egg from Kintobor's fridge, ensuring that Robotnik was never created, thus they had no self-destruct systems. They had also killed Sonic early on in this timeline. After retrieving the egg, Sonic and Chaotix travelled through time to the day Robotnik was created, and placed the egg back in the fridge, Sonic later giving a trailing wire a sharp tug to ensure that Robotnik came to be, and returned to the present day, where all was as it should be, bar the Miracle Planet still looking like a Metallix head. After conferring with Robotnik, Sonic and Chaotix were soon plunged back into battle with the entire Brotherhood, though Sonic was able to defeat them easily to taking advantage of their self-destruct system. Sonic himself noted that this was something of an anticlimax, though after the battle was over, Grimer approached Robotnik with the blueprint for a new Metallix design: A Knuckles model .
The Brotherhood had a backup plan however. In the event of their plans failing, the pirate Omni-Viewer would traverse time to bring multiple versions of Dr Robotnik and Sonic to one place. As Metallixes were created in both Robotnik and Sonic's names, the Emperor decided several versions of the two would be brought together to fight until the very time lines collapsed. This plan was brought to a halt by the present-day Sonic, with help from Vector the Crocodile and the real Omni-Viewer, who uploaded a much more benevolent program into the pirate Omni-Viewer. With all Sonics and Robotniks returned to their proper times, and the threat of the pirate Omni-Viewer eliminated, the Brotherhood of Metallix had finally been defeated for good.