Eight years after Harvey Dent's death, the Dent Act grants the Gotham City Police Department powers which nearly eradicate organized crime. Feeling guilty for covering up Dent's crimes, Police Commissioner James Gordon writes a resignation speech confessing the truth, but decides not to use it. Batman has disappeared; Bruce Wayne has become a recluse. Cat burglar Selina Kyle obtains Bruce's fingerprints from his home, kidnaps a congressman, then disappears. Selina hands Bruce's fingerprints to Phillip Stryver, an assistant to Bruce's business rival John Daggett, in hope of having her criminal record erased. Stryver double-crosses Selina, but she uses the congressman's stolen phone to alert the police to their location. Gordon and the police arrive to find the congressman, then pursue Stryver's men into the sewers while Selina flees. A masked man called Bane captures Gordon. Gordon escapes and is found by John Blake, a once-orphaned patrol officer who has deduced Batman's true identity from their similar backgrounds. Gordon promotes Blake to detective, with Blake reporting directly to him.
Wayne Enterprises is unprofitable after Bruce discontinued his fusion reactor project when he learned that the core could be weaponized. Later, Bane attacks the Gotham Stock Exchange, using Bruce's fingerprints in a transaction that bankrupts Wayne. Alfred Pennyworth, concerned that Bruce has not moved on from being Batman, reveals to him that Rachel Dawes had intended to marry Dent before she died; Alfred then resigns in an attempt to dissuade Bruce. Fearing that Daggett, Bane's employer, would gain access to the reactor, Bruce asks Wayne Enterprises board member Miranda Tate to take over his company. After being promised the software to erase her criminal record, Selina agrees to take Batman to Bane, but instead leads him into Bane's trap. Bane reveals that he intends to fulfill Ra's al Ghul's mission to destroy Gotham with the League of Shadows remnant. He engages Batman and delivers a crippling blow to his back, before taking him to a foreign, well-like prison where escape is virtually impossible. The inmates tell Bruce the story of Ra's al Ghul's child, born in the prison and cared for by a fellow prisoner before escaping—the only prisoner to have ever done so. Bruce assumes the child to be Bane.
Meanwhile, Bane lures Gotham police underground and collapses the exits. He kills Mayor Anthony Garcia and forces an abducted physicist, Dr. Leonid Pavel, to convert the reactor core into a nuclear bomb. Bane uses the bomb to hold the city hostage and isolate Gotham from the world. Using Gordon's stolen speech, Bane reveals the cover-up of Dent's crimes and releases the prisoners of Blackgate Penitentiary, initiating a revolution. The wealthy and powerful have their property expropriated, are dragged from their homes, and given show trials presided over by Dr. Jonathan Crane, where any sentence means likely death.
After months of recovery and re-training, Bruce escapes from the prison and enlists Selina, Blake, Tate, Gordon, and Lucius Fox to help stop the bomb's detonation. While the police and Bane's forces clash, Batman defeats Bane, but Tate intervenes and stabs Batman, revealing herself to be Talia al Ghul, Ra's al Ghul's daughter. Talia escaped the prison aided by her fellow prisoner and protector, Bane. She plans to complete her father's work by detonating the bomb and destroying Gotham, but Gordon blocks her signal, preventing remote detonation. Talia leaves to find the bomb while Bane prepares to kill Batman, but Selina kills Bane using the Batpod. Batman pursues Talia with the Bat, an aircraft developed by Fox, hoping to bring the bomb back to the reactor where it can be stabilized. Talia's truck crashes, but she remotely destroys the reactor before dying. With no way to stop the detonation, Batman uses the Bat to haul the bomb over the bay, where it detonates.
In the aftermath, Batman is presumed dead and is honored as a hero. With Bruce also presumed dead, Wayne Manor is left to the city to become an orphanage, and Wayne's remaining estate is left to Alfred. Fox discovers that Bruce had fixed the Bat's autopilot, and Gordon finds the Bat-Signal refurbished. While visiting Florence, Alfred witnesses Bruce and Selina together. Blake resigns from the police force and inherits the Batcave.