The cyborg Coton from the previous game defeated his opponents and faced the Supervisor, who used her morphing ability to defeat him and assimilate him into her own consciousness. Coton's thought patterns were cloned and used to bolster the artificial intelligence of the Supervisor, who also used fragments of his conscious in selected robots to imbue them with the ability to improve upon their own design. Electrocorp scientists, fearing that Coton had been defeated and that the Supervisor would now target the city, prepared a counter-virus based on EGO from the information Coton had earlier sent them. The Anarchy Virus was released to the main building of Electrocorp, and it infected most of the robots previously under Supervisor's control - the robots waged war against each other, disconnecting from the neuronet, quickly depleting the numbers of the Supervisor's army. Coton used the distraction caused by the malfunctioning robots to upload his consciousness to another robot, and prepared to either escape the Electrocorp building, or to attempt another attack on the Supervisor. At this point the story ends, and it is left open-ended -and dependent on the players ability- whether Coton is successful in either attempt.