The Brotherhood of Metallix is an army of Metallix robots created by Grimer. Led by an Emperor, the Brotherhood were charged with creating the ultimate Metal Sonic robot to destroy Sonic the Hedgehog, and remained aboard the Egg Fortress in the Special Zone after Robotnik had abandoned it. For reasons unknown, the Brotherhood went rogue and began working toward the conquest of Mobius.
Robotnik converted his old Egg Fortress base in the Special Zone into a Metallix factory, intending to leave the robots there to create the ultimate Metal Sonic. As a safety precaution, he built in a self-destruct program into their design. The Metallix secretly went rogue, calling themselves the Brotherhood and building an Emperor Metallix as they plotted to conquer Mobius themselves. They intended to capture the Omni-Viewer to achieve this, and paid Chaotix Crew member Nack the Weasel to help them. They contributed a new model of Metallix (based on Mecha Sonic from Sonic & Knuckles), to Robotnik's Death Egg II project.
This Metallix stole the Master Emerald and drew power from it to super-charge itself. It incapacitated Knuckles the Echidna, but made a fatal flaw in knocking Sonic onto the Emerald, allowing him to become Super Sonic. Super Sonic effortlessly ripped the Metallix to pieces.
Rise of the Brotherhood
Shortly after, thanks to Nack's assistance, the Brotherhood captured the Omni-Viewer. With Knuckles' help, Chaotix were able to get into the Egg Fortress and barely survived being slaughtered by a single Metallix. When the Brotherhood made it clear they intended to kill Nack as well, the turncoat brought out a neural disruptor cannon, which Knuckles used to seemingly deactivate the whole army. However, this turned out to have been anticipated by the Brotherhood, who had a back-up system that reactivated them all when the heroes had gone.
Unknown to the Crew, the Metallix had managed to create a pirate copy of the Omni-Viewer giving them the ability to travel through time and space. In their next move, the Brotherhood captured Grimer and charged him with building the Alpha Device, a device that could turn the Miracle Planet into a metallic power source once again. Robotnik pretended to need Sonic's help in destroying the Brotherhood, intending for the hedgehog and the Freedom Fighters to be killed in the attempt. Knowing they couldn't fight a whole planet of Metallixes, Sonic instead had Porker Lewis turn one into a walking bomb, wiping out the whole Brotherhood at once. However, the Emperor remained partially online, and Porker, trying to deactivate the Alpha Device, was trapped on the Miracle Planet when it vanished from Mobius' orbit.
Conquest of Mobius
During the month away from Mobius, the Emperor was able to rebuild his army and transform the planet. A new model of Metallix was created that could disguise itself as Porker, so as to keep Sonic away from the Miracle Planet while they left to change Mobius' history. Chaotix, however, were sent to investigate, and both took Sonic to the planet and helped destroy this Metallix. The heroes managed to rescue the real Porker, but then the terrifying truth became apparent - the Metallixes had changed history, and Mobius had become a city-planet, covered with filthy industry, where surviving Mobians lived underground. The reason for the change soon became apparent, as Sonic and Chaotix attempted to fix the time line - the Brotherhood of Metallix had traveled back in time to the point of Doctor Robotnik's creation, and removed from the fridge the rotten egg that would transform Doctor Ovi Kintobor into Ivo Robotnik. Kintobor never became Robotnik, and the Metallixes, created by Grimer alone, ruled the planet.
Retrieving the egg, Sonic and Chaotix returned to Kintobor's lab and replaced it, and then, as Kintobor held it in his hand, Sonic yanked a cable to trip him up, triggering the chain of events that turned him into Doctor Robotnik. Despite the disturbing revelation that he was responsible for creating the greatest evil on Mobius, Sonic returned to the present with Chaotix, where the robots still held control of the Miracle Planet. Forced into an alliance with Doctor Robotnik, Sonic retrieved a device from the villain that deactivated all the Metallixes in a pitched final battle (Sonic later claimed that he found it anticlimactic that the Emperor Metallix and his army were defeated by a simple push of a button).