In the present, Ducard asks Bruce if he still feels responsible for the death of his parents. Bruce responds that his is far too angry to feel guilty. His training with the League of Shadows begins. He is trained in the arts of ninjutsu, stealth, combat theatricality and deception.
Bruce is trained not only to fight 6 men but to 'engage 600.' Ducard enforces his belief that all forms of crime must be fought without mercy and pity. Ducard explains that his wife was murdered and that he joined the League when he achieved his vengeance. Bruce reveals that he can't claim his vengeance.
Flashback, three years earlier: 14 years after his parents were killed, Bruce arrives at Wayne Manor from Princeton University; he's come home for Joe Chill's parole hearing. Alfred still manages the house and expresses his concern over Bruce. Rachel is now an Assistant District Attorney and takes Bruce to the hearing.
Unknown to her, Bruce is concealing a revolver, with which he plans to shoot Chill down if he is released. In the hearing, Chill expresses remorse for the murder of Bruce's parents and is given parole should he testify against his cellmate, gang boss Carmine Falcone (Tom Wilkinson).
However, before Bruce can act, a female assassin posing as a reporter comes up with a pistol in hand and shoots Chill. Bruce watches as Chill bleeds to death and the assassin is arrested. Driving away after the incident, Rachel lectures Bruce afterward on the difference between justice and revenge and reveals that Gotham City is still suffering because of Falcone's illegal drug empire.
Rachel then slaps him harshly when he reveals that he was planning to shoot Chill. She tells him that his father would be ashamed of him. Bruce, convinced that he has nothing to lose, makes his way to a bar in the Gotham underworld to confront Falcone.
Falcone brags about his control over the city's police and judges, even pointing out who he has in his pockets who is present. He then threatens Rachel and Alfred to prove that Bruce does have a lot to lose. His thugs beat up Bruce and he leaves. Left no other choice but to run away, Bruce stows away aboard a cargo ship leaving the port.
Bruce is then shown in China stealing food to survive and eventually getting involved in gangster operations in order to infiltrate them. He is then arrested - ironically, in the act of stealing Wayne Enterprise crates - and sent to the prison Ducard discovered him in at the beginning.
In the present, when Bruce reaches a skill level in which he is an equal to the majority in the League, he faces Ducard in combat. However, he is exposed beforehand to the vapors of the blue flower he brought up to the mountain earlier. The smoke distorts his senses and makes him hallucinate about bats, his greatest fear.
Bruce overcomes his phobia and employs a clever trick to best Ducard in a sword fight, passing the trial. Ra's al Ghul sends for him and Ducard. Ra's puts Bruce to one final task before becoming a full member of the League. The task is to execute a prisoner of the League -- a man who has stolen his neighbour's land and killed them. Bruce refuses.
Ra's reveals to Bruce that he has been trained in order to lead the League to Gotham City, which is corrupted by evil to such an extent that it must be razed. Bruce sets a diversion, and lights the League's headquarters on fire and is forced to fight al Ghul while the the rest of the League escapes the wreckage to safety.
Ducard is knocked out by Bruce who then manages to fend off Ra's, who is killed instantly when a roof beam collapses on him. Bruce picks up an unconscious Ducard and rescues him from the building as it explodes. Bruce leaves Ducard in the care of a villager.
Bruce contacts Alfred, who arrives in a private jet to pick him up. Alfred reveals that Bruce, who has been away for seven years, has been legally declared dead by William Earle so that Earle can take Wayne Enterprises public.
Bruce says it's a good thing he willed everything to Alfred, who jokes that Bruce is welcome to borrow the Rolls-Royce....so long as he brings it back with a full tank. Bruce explains to Alfred a plan he has to fight the Gotham underworld by taking on a new persona, which all criminals will fear.
In Gotham, a serial killer named Victor Zsaz (Tim Booth), who is allegedly insane, is being transferred from a regular prison to the Arkham Asylum on the opinion of Dr. Jonathan Crane (Cillian Murphy). Rachel challenges this as Zsaz is yet another one of Falcone's thugs that Crane has had moved to the Asylum and away from prison, and goes unnoticed due to Falcone's corrupt influence.
Dr. Crane meets with Falcone later on that night and demands that Rachel be dealt with. When Falcone refuses, Crane threatens him with the knowledge that his unknown boss is coming to the city.