Rise Of The Brotherhood
The Emperor Metallix made its first appearance in Total Chaotix. It had sent its minions to hijack the Omni-Viewer, which they had easily accomplished despite the presence of Knuckles the Echidna and the Chaotix. The Emperor had also hired the services of Nack the Weasel in order to lure the Chaotix into a trap. When the heroes invaded the Egg Fortress, Nack delivered them straight into the Emperor's hands, but was immediately betrayed after finishing his job. Nack attempted to destroy the Emperor with a shrunken disruptor weapon concealed in his hat, but a Metallix drone shot him. Knuckles managed to grab the disruptor and fired it at the Emperor and his guards, deactivating them. When the heroes had left with the Omni-Viewer and their traitorous cohort, a back-up system engaged and the Metallix came back online. Worse, they had copied the Omni-Viewer's program and created a pirate copy, giving them access to all of time and space.
Almost immediately after their encounter with the Chaotix, the Brotherhood put their Omni knock-off to work. They captured their creator Grimer and forced him to create the key to their dominace of Mobius: the Alpha Device. After forging a temporary truce with Robotnik, Sonic went into the Special Zone to find Grimer. When Sonic snatched the Alpha Device, the Emperor threatened to kill Grimer if the hedgehog didn't hand it over. Sonic yielded and gave up the device, then the Emperor departed for the Miracle Planet. When he arrived, he and the other Metallix transferred much of their own energy to the Alpha Device. Once the device was fully charged, the Emperor planted it in the ground and it began to slowly mechanize the land. When Sonic and the Freedom Fighters arrived, the Emperor sent a single Metallix to hunt them down. The robot was deactivated and Porker Lewis was able to jury-rig it to walk into the Brotherhood's midst and self-destruct. The explosion was powerful enough to destroy most of the Metallix drones, but the Emperor just managed to survive though only its upper body remained active. The Alpha Device also survived the explosion and Porker tried to shut it down. However, the Emperor managed to stop him and keep the device operational. Sonic and the others did not see this as they had to flee before the Miracle Planet left Mobius' orbit.
The Age Of The Brotherhood
With Porker captured and the Alpha Device secured, the Miracle Planet's terraforming proceeded as planned. The Emperor repaired itself and rebuilt its army, which grew larger and stronger now that the Miracle Planet had been remade in their image. The planet was cloaked to appear normal with no evidence of the Metallix's presence, and so the Emperor and his forces initiated their conquest of Mobius. With the Pirate Omni-Viewer, the Brotherhood travelled back in time and stopped Doctor Ovi Kintobor from ever becoming Robotnik (they did this simply by removing the rotten egg from Kintobor's refridgerator). With Robotnik removed from the timeline, the Brotherhood were safe from being destroyed by their self-destruct mechanism (which for some reason they could not remove). They systematically began exterminating all life across the planet and mechanizing it the same way they had the Miracle Planet. However, all of the damage they had done was prevented by Sonic and the Chaotix, who travelled through time and made sure that Robotnik's creation occurred. With Robotnik's existence secured, his contribution to Grimer's Metallix project went ahead as normal. The Emperor then led his entire army to attack Citadel Robotnik and attempted to stop the doctor from activating the self-destruct program. The Emperor grabbed the doctor and almost crushed the self-destruct trigger, but Sonic grabbed it and pushed the button. With the push of that button, the Brotherhood of Metallix was destroyed.
In Issue 255 of Sonic the Comic Online, a picture of the Emperor was seen in a single panel, revealing it to be the real villain behind the story's events. Despite being destroyed, the robot had pre-programmed into the Omni-Viewer's pirate copy instructions to bring different versions of Sonic and Robotnik throughout time together and have them destroy one another. A message recorded by the Emperor states both the irony that they had both been responsible for it's creation (Robotnik ordered Grimer to create it, while it's design was based on Sonic) and how the plan for Sonic and Robotnik to kill one another was to be initiated only if the Brotherhood of Metallix was defeated indefinitely.
Aside from having complete control over its hordes of Metallix drones, the Emperor Metallix has no special abilities. It clearly wasn't designed for combat as it has no weapons and it certainly can't match Sonic's speed like its minions can. It is highly intelligent, however, creating various schemes which are on par with if not superior to those of Robotnik's own.