Bruce Wayne was murdered alongside his parents by Joe Chill. The shock gave Alfred a heart attack that killed him.
With the Waynes gone, Rupert Thorne took control of Wayne Enterprises through a series of backstabbing plots and managed to run Gotham City's economy into the ground, making the city a living hellhole. In the middle of the chaos, Lucius Fox is fired and dies in poverty.
Captain James Gordon becomes depressed after his daughter is murdered by Jason Todd, a small-time hoodlum, and has a nervous breakdown. After murdering his pregnant wife Barbara, Gordon goes to the police station, kills several colleages, including Harvey Bullock, Jim Corrigan, Renee Montoya and Crispus Allen, and then commits suicide.
With the police force in chaos, riots begin to tear the city apart. Tim Drake and Stephanie Brown, who go to school together, are killed by a bomb thrown by a terrorist, alongside several other teenagers.
Eventually, there's a mass breakout at the Arkham Asylum and all it's criminals begin a murder spree of unseen proportions. A circus is attacked, and Dick Grayson dies protecting his family of Victor Szasz. With no other option, the government isolates the few citizens left alive and drops a series of refined bombs into the city that kills all it's remaining inhabitans.
