Some time after the events of Season 1, inspector Tsunemori, now the senior inspector in her old team, commands several new inspectors and enforcers. A disturbing series of bombings becomes their baptism of fire.
The bomber is captured, but his high crime coefficient becomes normal again, which should be impossible. Inspector Tsunemori discovers letters "WC" scratched on her window. Inspector Shisui and her gun are missing.
Inspector Tsunemori starts to believe that the missing inspector has been kidnapped by a person who can't be read by the psycho-scanners. Since this should be impossible, she asks Jouji Saiga, who's now locked up, for help.
An agile murderous psychotic elderly man has trapped Inspector Aoyanagi and several patients. His Crime Coefficient somehow remains clear no matter how brutal he becomes, so she can't use her Dominator. She becomes the bait for the MWPSB.
A man known as Kamui brainwashes Inspector Shisui and is able to wield her Dominator. The other inspectors close in on his suspected position, but it's just another deadly trap. Hacked sentry mechs from a nearby factory target them.
The hack made the mechs controllable by unsuspecting citizens who think they're playing their favorite handheld game. If the inspectors shut down the system, mass hysteria and rise in Crime Coefficients are inevitable.
The team apprehends the doctor who operated on Kamui as a child and learn more information about Kamui's motivations. Meanwhile, Inspector Mika, who hates Inspector Tsunemori, finds out on her own more than she bargained for.
Sinister chief Kasei and sadistic enforcer Togane tell nosy Inspector Mika all about Sybil and make her their pawn. Meanwhile, Inspector Tsunemori's team tracks down a person who might be helping Kamui.
Kamui makes his final move, so chief Kasei orders Inspector Tsunemori to kill him and sends enforcer Togane to force her to do it by any means necessary. Inspector Tsunemori is about to found out what color she truly is.