In Uzbekistan, Bane, a mysterious terrorist figure and former member of the League of Shadows, abducts nuclear physicist Dr. Leonid Pavel from a CIA aircraft.
Eight years after the death of District Attorney Harvey Dent, Batman has disappeared and organized crime has been eradicated in Gotham City thanks to the Dent Act giving expanded powers to the police. Commissioner James Gordon has kept Dent's murderous rampage a secret and allowed blame for his crimes to fall on Batman. He writes a resignation speech revealing the truth, but decides that the city is not yet ready to hear it. Bruce Wayne has become a recluse, and Wayne Enterprises is losing money after Wayne discontinued his fusion reactor project when he learned that it could be weaponized.
Six months following Pavel's kidnapping, Bane sets up his base in the city sewers, and prompts Wayne's corporate rival John Daggett to buy Wayne's fingerprints. Cat burglar Selina Kyle obtains Wayne's prints from Wayne Manor for Daggett, but she is double-crossed at the exchange, therefore she alerts the police. Gordon and the police arrive and pursue Bane and Daggett's henchmen into the sewers while Selina flees. The henchmen capture Gordon and take him to Bane. Gordon escapes and is found by rookie officer John Blake. Blake, a fellow orphan who deduced Bruce's secret identity, confronts Bruce and convinces him to return as Batman. Bane later attacks the Gotham Stock Exchange by using Wayne's fingerprints in a series of transactions that leaves Wayne bankrupt; Batman resurfaces for the first time in eight years while intercepting Bane and his subordinates. Wayne's butler, Alfred Pennyworth resigns in an attempt to save Bruce from death at the hands of Bane. Wayne finds comfort in new Wayne Enterprises CEO Miranda Tate. Using the stolen transactions, Bane expands his operations and kills Daggett.
Kyle 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. Batman fights Bane, but Bane beats him; dealing a crippling blow to his back before taking him abroad to an underground prison. There, the inmates tell Wayne the story of Ra's al Ghul's child, who was born and raised in the prison before finally escaping the only prisoner to have done so. Bane lures Gotham's police into the underground sewer network and uses explosives to trap them, and destroy the bridges surrounding the city. He kills Mayor Anthony Garcia and forces Dr. Pavel to convert the reactor core into a decaying neutron bomb at a football stadium before killing him as well. Bane reads Gordon's speech to the public, and releases the prisoners of Blackgate Penitentiary, initiating chaos while holding the city hostage and isolated with the bomb.
Months later, a recovered Wayne escapes from the prison and returns to Gotham. Batman frees the trapped police and they clash with Bane's army in the streets; during the battle, Batman manages to overpower Bane. Tate intervenes and stabs Batman, revealing herself to be Talia al Ghul, Ra's al Ghul's daughter. She activates the bomb's detonator, but Gordon blocks her signal. Al Ghul leaves to find the bomb while Bane prepares to kill Batman, but Kyle arrives and kills Bane. Batman and Kyle pursue al Ghul, hoping to bring the bomb back to the reactor chamber where it can be stabilized. Al Ghul's truck crashes, but she remotely floods and destroys the reactor chamber before dying. With no way to stop the detonation, Batman uses his aerial craft, the Bat, to haul the bomb far over the bay, where it safely explodes. Before takeoff, Batman reveals his identity to Gordon.
In the aftermath, Batman is presumed dead and is honored as a hero. With Wayne presumed dead as well, Wayne Manor becomes an orphanage and his remaining estate is left to Pennyworth. Gordon finds the previously destroyed Bat Signal repaired, while Lucius Fox discovers that Wayne had fixed the previously malfunctioning auto-pilot on the Bat. Blake resigns from the police force and a parcel left to him in Wayne's will leads him to find the Batcave. While visiting Florence, Pennyworth discovers that Wayne is alive, and in a relationship with Kyle.