The film's entire narrative is built on a labyrinthine conspiracy surrounding the billion-dollar 'Renewal' fund established by Thomas Wayne. It is eventually revealed that the late Thomas Wayne, desperate to protect his wife Martha's history of mental illness from being leaked by a reporter, turned to mob boss Carmine Falcone to quietly intimidate the journalist. Falcone instead murdered the reporter, creating a blackmail scheme that effectively allowed him to control Gotham's elite.
Following the Waynes' murders, Falcone and corrupt city officials embezzled the massive Renewal fund, using it to run the city's criminal enterprises. The Riddler (Edward Nashton), who grew up in the horrific squalor of a Gotham orphanage deprived of these exact funds, discovers this truth and orchestrates a series of gruesome murders to expose the corruption to the public.
In the third act twist, the Riddler voluntarily allows himself to be arrested, revealing his master plan from within Arkham Asylum: he has positioned vans filled with explosives to destroy Gotham's seawalls and mobilized an army of radicalized internet followers to assassinate the surviving political leaders. The seawalls break, catastrophically flooding the city. In the climax, Batman defeats the zealots but realizes he cannot just be a terrifying force of vengeance. He must be a savior. He leads the trapped citizens out of the flooded arena using a glowing red flare, symbolizing his ultimate transformation into a beacon of hope.