In Angel Devoid: Face of the Enemy, which is set in the futuristic NeoCity of the year 3032, the player takes the role of Jack Hard, a cop whose life goal is to hunt the criminal Angel Devoid. After an accident during a car chase he awakens in an hospital - only to find out that his face was operated to look like his eternal enemy. Now he is a wanted man...

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.

On June 6, 1996 (1991 in the Japanese versions), a biological weapon known as Lucifer-Alpha under development in Chernoton, Russia, is released into the atmosphere, resulting in the death of 80% of the Eurasian population which in turn results in the death of half of the world's population. The contaminated area becomes uninhabitable for a decade, when Lucifer-Alpha mutates into a non-lethal form. This tragic event later becomes known as "the Catastrophe". Fifty years later, in 2047 (2042 in the Japanese versions), a breed of artificial life-forms or bioroids known as "snatchers" began appearing in the artificial island of Neo Kobe City, killing their victims and taking their place in society. Nobody knows exactly what they are or where they come from. As Gillian Seed, an amnesiac working for an Anti-Snatcher task force called J.U.N.K.E.R., the player's goal is to track down the source of the snatchers and discover Gillian's mysterious connections with them. The story takes place in three acts.