Mobius is at peace, Dr Robotnik having been taken prisoner by the enigmatic Prosecutor of the Drakon Empire. Unfortunately, a Mobius Ring appears in the sky of Emerald Hill Zone, and Robotnik emerges from it, flanked by two Badniks. Elsewhere in the Control Centre, Sonic, Tails and Amy transfer the Kintobor Computer from the laptop to a new system. Kintobor links up with the network of sensors around the zone, enabling him to warn the Freedom Fighters if the zone is attacked. Unfortunately, before he can get to grips with it, Robotnik arrives. The dictator elaborates that the Drakons recognised his intellect, and they have made a deal. The Badniks take out Tails and Amy, but before Sonic can attack, Robotnik reveals his trump card: A new Metallix, styled after Knuckles. Unlike his predecessors however, this Metallix is loyal only to Robotnik, but is just as powerful, and the robot easily incapacitates Sonic. Robotnik summons the Mobius Ring, and he and the Metallix exit through it, taking an unconscious Sonic with them. Before the ring disappears however, Tails stirs and follows them.
In the Drakons' House of War, Sonic is been brought before Emperor Ko-Dorr for crimes against the Drakon Empire. Robotnik is present, but seems to know something Sonic doesn't, and claims he is only there to see that justice is served. Sonic tries to retaliate in force, but a Sentinel shocks him into submission. At the mere mention of the word 'Sentinel', a memory stirs within Sonic, which Robotnik seems to have been waiting for: Sonic remembers the giant Sentinel statue in the Aquatic Ruin Zone, and its immediate collapse. The hedgehog is accused of destroying it, but denies it, and is more concerned with why it was there in the first place. Ko-Dorr reveals that the Drakons used to live in the zone, but now realise it was a mistake for them to leave Mobius, as it has apparently become a threat to them. Sonic is outraged, but the Emperor is hearing none of it, and orders Sonic to be taken away. That evening, as Sonic is trying and failing to break down the walls of his cell, Robotnik comes in to gloat and tell Sonic of his upcoming trial: Trial by combat. As Robotnik leaves, Tails appears at Sonic's window. They discuss Sonic's situation, and are unable to come up with a solution. Elsewhere, Robotnik and Grimer make plans for Mobius, but they have a higher priority: Watching Metallix finish Sonic off in the trial.
The following morning, Sonic enters the Arena of Judgement to stand trial, while a desperate Tails lurks in hiding. Sonic is understandably impatient and vows to Robotnik that even if he doesn't survive, Mobius is ready for another attempted takeover. Robotnik however, is immensely confident in his new alliance, but is reminded by Ko-Dorr to stick to his side of the agreement when the time comes. Metallix, appointed as a temporary Prosecutor enters and the trial begins. Sonic and Metallix recieve a weapon each and begin to clash. The hedgehog quickly works out that speed and agility are needed to wield such weapons properly; two traits he easily possesses. He knocks Metallix flying, but just as he thinks he's won, the robot takes a shot at Sonic with its death ray, which Sonic fortunately doesn't take the full blast of. With Sonic down, the Emperor declares him guilty, but before Metallix strikes the killing blow, Sonic is back on his feet and fighting again. Outside, the citizens of the Drakon Empire are watching the trial live on giant screens, Tails among them in disguise. As Metallix fights back, Tails struggles to think how he can help Sonic.
Tails slips into the Arena and prepares to knock out the lone Sentinel guarding the main entrance. In the ring, Sonic is struggling against Metallix, who keeps coming no matter what. Suddenly Tails gets the entrance open and calls Sonic over. Metallix charges at them, but Tails, seeing that Sonic's in no fit state to fight back, brings the door down upon the robot, crushing it into submission. Sonic recovers, stating that he could have taken Metallix out without Tails, which the fox confirms. Without warning, a Prosecutor attacks, but Sonic, back to full strength, launches a violent assault on it, ploughing through its chest and knocking its helmet off, revealing the Drakons' true form: Fish-like creatures operating robot bodies to traverse the land. More Prosecutors arrive, accompanied by an enraged Robotnik. Before another fight can break out, Ko-Dorr arrives stating that Sonic is innocent, having won his trial by combat. Robotnik doesn't accept this, since the hedgehog was helped, but he is immediately overruled by the Emperor. A Prosecutor prepares a Mobius Ring to get Sonic and Tails home safely, but Sonic vows that the Drakons are his enemy and haven't seen the last of him, as long as they support Robotnik.
The Evil Empire was reprinted in its entirety in Issue 223, the final issue of Sonic the Comic.