The film begins with a group of CIA agents climbing on board a small plane with some hooded prisoners and Professor Achilles Milo, a physicist. The agents interrogate the prisoners for information on a mercenary named Bane. One of them begins to speak and his hood is removed, revealing a masked man. He tells the agents that he planned on getting caught and the next step is to crash the plane. He suddenly activates a tube which pumps a drug known as Venom into him, enhancing his strength. He quickly breaks his handcuffs. At the same time, a cargo plane appears above the plane and several men on zip lines dive onto the CIA plane, shooting the windows out. Bane takes Milo and gives him a blood transfusion with a dead man, making it appear as if the other man is Milo. They then leap from the plane and return to the cargo plane as the CIA plane falls to the ground and explodes.
Eight years since the death of Harvey Dent, Gotham City is at peace. Bruce Wayne throws a party in honour of Dent's memory. He overhears police captain Harvey Bullock discussing Mayor Hamilton Hill's plan to retire Police Commissioner James Gordon, calling him a war hero in peace times. Bruce goes to his quarters and encounters a maid, Selina Kyle, who tries to play innocence but he recognizes her as a thief, having stolen his mother's pearls from a safe. She manages to escape through a window.
A young police officer, Terry McGinnis, finds the body of a missing boy from the local orphanage where he grew up. While visiting the orphanage for information, McGinnis learns that the boy heard of possible work in the sewers and went looking for it, and presumably drowned. McGinnis decides to investigate the supposed work. Gordon goes with him but they get into a shootout with a gang of mercenaries, during which Gordon is wounded and captured. McGinnis manages to flee as the mercenaries bring Gordon before their leader; Bane. Bane orders him to be searched and they find a speech that Gordon wrote but never gave, which reveals the truth about the death of Harvey Dent. Gordon manages to fall into a water way and is carried away to safety, where he is found by McGinnis and brought to hospital.
Bruce learns of Gordon's shooting and his babbling of an underground army, and decides that it's time to return as Batman to fight this new threat. He approaches Lucius Fox, who reveals to him a large aircraft called the Batwing. He visits Commissioner Gordon wearing a ski mask to learn about Bane and then researches him, learning that Bane was excommunicated from the League of Shadows by Ra's al Ghul. Alfred tells Bruce that if Bane was too extreme for Ra's al Ghul, who is not a threat to be taken lightly.
That evening, Bane and his men arrive at the Gotham Stock Exchange and try to rob it, while the police gather outside. When their cyber theft is foiled, Bane and his men take hostages and escape on motor cycles. The police chase them through a tunnel when suddenly Batman appears on the Batcycle. With Bane almost out of reach, Bullock orders the police to chase Batman. Batman pursues Bane and rescues the hostages but the mercenary escapes. Back at the Batcave, a worried Alfred tells Bruce to leave Batman behind, revealing that Vicki Vale chose Harvey Dent over Bruce prior to her death in the previous film before he resigns.
Fox informs Bruce that Bane's hit on the stock exchange has left Wayne Enterprises bankrupt. They take businesswoman Vesper Fairchild to see a clean energy fusion reactor they were working on, and ask her to take over as Wayne Enterprises CEO to protect it and keep it out of the hands of Roland Dagget, an employee who is working with Bane. At the next meeting, Vesper is appointed, enraging Dagget. Returning to his penthouse in a fury, he is confronted by Bane, who he berates, telling him that he gave him money. Bane thanks him but tells him that he has serviced his purpose, before throwing Dagget through a window to his death.
Bruce finds Selina at her apartment and asks her about Bane, and she reveals that she can help him. They organize to meet that night in the sewers. Returning home in a cab, Bruce meets Vesper at Wayne Manor and after going inside, they sleep together. While Vesper is sleeping, Bruce puts on the Batsuit and goes to meet Seline, dressed in her own costume as the Catwoman. However, Catwoman reveals that she was forced by Bane to betray him and he is locked in with Bane, who savagely beats him and breaks his back while Selina flees.
The next day, McGinnis tails Selina to the airport, where she is trying to flee. He corners her in an airport administration office and asks her why she's trying to leave. She tells him that she's trying to escape from Bane. Selina is arrested and put in Blackgate Prison.
Bruce wakes up in an underground prison, with Bane standing over him. Bane tells him that he owns the prison, and that he will use it to torture Bruce rather than outright kill him. Bruce asks how, and Bane reveals a monitor with a live news feed. Bane then tells him that Gotham will soon burn.
Back at Wayne Enterprises, Vesper and Fox are taken hostage by Bane and his men, who forces them to reveal the location of the reactor, where he has Milo convert it into a fully primed nuclear bomb with a six metre blast radius. From his hospital bed, Gordon decides that in the wake of the attack on the stock exchange, Bane needs to be smoked out. Remembering enough about Bane's base of operations, he realises that will it take the entire police force to be able to combat Bane's mercenaries. While Bullock organizes the police, McGinnis and Gordon research Daggett's assets and they learn of his cement plants around the city. McGinnis heads to one such sight and recognizes one of the workers as a truck driver who caused a roadblock during the stock hit. McGinnis realises that he is in fact working with Bane and is attacked by another worker. McGinnis manages to fire his gun, which ricochets off of a truck and kills one of them before the other falls into a pit and is buried alive under cement. As he searches the plant, he realises, to his horror, that Bane has rigged the entire city with C4 explosives.
As thousands of police officers swarm into the underground via sewer and subway entrances, Mayor Hamilton Hill is amongst the hundreds of civillians attending a football game in the stadium. During the National Anthem, Bane and his men arrive via the boiler room and await the kickoff. As the game begins, he detonates the explosives spread across the city, destroying all but one bridge connecting the city to the rest of the world, as well as the stadium, swallowing most of the players and blowing up the mayor's box, killing him. Deep underground, the police hear the muffled explosions and all of the entrances caving in, trapping them.
McGinnis arms himself with a shotgun and heads for the hospital, where some of Bane's goons have arrived to take Gordon. After a shootout, he rescues Gordon and they head for safety in McGinnis' apartment. Meanwhile, at the stadium, Bane introduces Milo, who explains that he is the only one capable of disarming the bomb before Bane snaps his neck, killing him. He then explains that an anonymous Gothamite is carrying the trigger, and if anybody tries to flee Gotham or the outside world intervenes, the bomb will go off. The remaining bridge is sued to bring in food and other resources, but the government is forced to guard it in case anyone tries to escape and the bomb is detonated.
The following day, Bane marches to Blackgate Prison where he publicy reads Gordon's speech, revealing the truth about Harvey Dent. The citizens begin to agree with Bane and storm into the prison to free the prisoners who have been illegally detained by the Dent Act, who then allign with Bane and hold kangaroo courts to decide the fate of those opposed to their reign.
Over the following months, Bruce begins to get himself back into shape. He learns from a doctor in the cell next to his that many years ago, a young mecenary who was actually Ra's al Ghul had an affair with a local warlord's daughter. The warlord arrested Ra's and planned to put him in the prison, but Ra's escaped and fled, promising to one day return for the girl. However, the girl's father instead put her in the prison, where she gave birth to Ra's' child before she was killed by the other inmates. Bruce watches as many men try to climb out of the prison via a hole at the top, but they always fall. He too tries, but fails twice. He then learns from the doctor that the child of Ra's al Ghul, who he believes to be Bane, was the only person to ever escape from the prison by climbing without the safety rope. Bruce also tries without the rope and succesfully escapes before heading back to Gotham.
Back in Gotham, Gordon, McGinnis, Fox and Vesper have been tracking three trucks constantly on the move as one of them contains the bomb and they are trying to figure out which. Bruce arrives and meets Selina, finally convincing her to help him in his final effort against Bane. He gets Fox and they break into his own armoury, where he retrieves another Batsuit, and then meets Gordon, saving him from Bane's thugs. However, McGinnis has remained in contact with his partner, trapped underground, and they find a way out, but they are caught and his partner is shot. Batman arrives just in time to save him and he then uses the Batwing to liberate the police. Meanwhile, Bane, knowing that Bruce has returned and will come for Vesper, has her taken to city hall, where he is holed up.
The next morning, McGinnis evacuates the orphanage onto a bus and takes them to the bridge, where he gets into a confrontation with a government agent who has strict orders to not let anyone cross, culminating in the agent before forced to blow part of the bridge. Selina takes the Batcycle to open another tunnel in case evacuation in needed. Gordon has Bullock rally the entire police force and they march down the street towards city hall, where Bane orders his men to use a tank to kill them. Suddenly, the Batwing appears and destroys the tanks, allowing the police to charge straight at Bane. Batman then gets out and joins the brutal melee, and becomes involved in a brawl with Bane, where he manages to sabotage his Venom supply. Batman drags him into city hall and is forced to break his neck, paralyzing but not killing him.
Batman demands that Bane tell him who has the trigger, but Bane tells him that he's too late. When Batman mentions being the child of Ra's al Ghul, Bane says that he never did actually escape the prison. Suddenly, Vesper stabs Batman in the back. She reveals that her real name is Talia al Ghul; in the prison, Bane protected Talia and after she escaped, she sought out her father and they returned to free Bane, but when they revealed their plan to be together, an enraged Ra's had Bane attacked and his face was disfigured before he excommunicated, but as result of her father's actions Talia abandoned the League of Shadows. She admits that she is the triggerman but reveals it doesn't matter; they had previously removed the core from the bomb, making it highly unstable, and detonation is imminent. She then leaves, taking the truck carrying the bomb. Bane tells Batman that he has failed and then finishes twisting his own neck, killing himself.
Outside of city hall, Fox arrives in the Batmobile as does Selina on the Batcycle. Batman takes the Batmobile and he and Selina embark on a city wide high speed pursuit of the truck carrying the bomb, eventually causing it to crash. Talia tells Batman that she has fulfilled her father's destiny and that Gotham will soon be destroyed. She makes a final grab for a weapon with which to kill Batman, but is fatally shot by Gordon. Realising that not long is left on the timer, Batman kisses Selina and then attatches the bomb to the Batwing. As he prepares to fly it out over the bay, he reveals his true identity to Gordon, shocking him. On the bridge, McGinnis and the kids watch as the Batwing flies into the horizon and cheer, until the bomb goes off and a huge mushroom cloud appears in the distance.
In the aftermath, a private funerl is held for Bruce Wayne, and it is officially declared that Bruce died trying to defend his parents legacy from Bane's thugs. A statue is erected in honour of Batman. Wayne Manor is left to the city, and is turned into an orphanage. Alfred inherits the fortune. McGinnis is surprised when he is left a duffel bag.
Fox learns that the autopilot on the Batwing, previously found to be faulty, was fixed some months prior to Bane's takeover. Gordon discovers a repaired batsignal after he destroyed it at the end of the previous film. Alfred, in Florence, spots Bruce sitting at an adjacent table with Selina Kyle, and they exchange a simple nod of acknowledgement.
McGinnis finds that the duffel bag contains a GPS system with coordinates and a rope. He follows them and finds a large waterfall, which he uses the rope to swing through into a cave where he unsettles a flock of bats. McGinnis looks around him and realises that he is in the Batcave, and smiles.
Eric Bana - Bruce Wayne/The Batman
Geoffrey Rush - Alfred Pennyworth
Bryan Cranston - Commissioner James Gordon
Jared Padalecki - Terry McGinnis
Billy Dee Williams - Lucius Fox
Olivia Wilde - Selina Kyle/Catwoman
Arnold Vosloo - Ra's al Ghul
Olga Kurylenko - Vesper Fairchild/Talia al Ghul
Nathan Jones - Antonio Diego/Bane
Michael Fassbender - Harvey "Two-Face" Dent