After a series of unsuccessful projects to resurrect Batman on screen following the 1997 critical failure of Batman & Robin, Nolan and David S. Goyer began work on the film in early 2003 and aimed for a darker and more realistic tone, with humanity and realism being the basis of the film. The goal was to get the audience to care for both Batman and Bruce Wayne. The film, which was primarily shot in England and Chicago, relied on traditional stunts and miniatures—computer-generated imagery was used minimally. A new Batmobile (called the Tumbler) and a more mobile Batsuit were both created specifically for the film.

Batman Begins was critically and commercially successful. The film opened on June 15, 2005 in the United States and Canada in 3,858 theaters. It grossed $48 million in its opening weekend, eventually grossing over $372 million worldwide. The film received an 84% overall approval rating from Rotten Tomatoes. Critics noted that fear was a common theme throughout the film, and remarked that it had a darker tone compared to previous Batman films. A sequel titled The Dark Knight was released in July 2008 and also saw the return of both Nolan and Bale to the franchise.

A young Bruce Wayne falls down a well and is attacked by bats. Bruce then awakens from this nightmare of his past and is revealed to be a prisoner in Bhutan. He is approached by Henri Ducard, who speaks for Ra's al Ghul, leader of the League of Shadows, and invites him to train with the elite vigilante group. Returning to his childhood, as Bruce leaves an opera with his parents they are murdered by a mugger named Joe Chill. Chill is later arrested and Bruce is taken home and raised by the family butler Alfred Pennyworth.

Years later, Bruce returns to Gotham City from Princeton University, intent on killing Chill, whose prison sentence is being suspended in exchange for testifying against crime boss Carmine Falcone. Before he can act, however, one of Falcone's assassins kills Chill. Rachel Dawes, Bruce's childhood friend and now an assistant district attorney, is disgusted with Bruce's intent, so he confronts Falcone. After this, Bruce decides to travel the world for several years, learning the various ways of the criminal underworld, before himself becoming a criminal and being arrested. After Bruce's training in the League of Shadows, Ra's and Ducard tell Bruce his purpose: that he must lead the League to destroy Gotham, believing it is corrupt beyond saving. Bruce refuses to become a murderer and battles Ra's, burning the temple in the process, before making his escape. Ra's is killed by falling debris, but Bruce saves an unconscious Ducard and returns to Gotham.

Falcone now dominates the city. Bruce enlists the help of Sgt. Jim Gordon, one of the city's few honest police officers, and befriends Lucius Fox, a former board member of Wayne Enterprises. Fox helps Bruce acquire a prototype armored car and an experimental armored suit. With Alfred, Bruce finds another entrance to the cave under the well and creates a workshop, modifying his equipment to take up the identity of Batman. An illegal drug shipment is infiltrated by Batman, who then captures Falcone and provides Rachel with evidence capable of indicting him. Falcone and his men are transferred to Arkham Asylum with the help of Dr. Jonathan Crane, who has been paying off Falcone to ship the drugs, containing a toxic hallucinogenic, into Gotham City. However, Dr. Crane induces Falcone with the same toxin that literally drives him insane with fear. While investigating the drugs, Batman encounters Crane, who also sprays him with the fear toxin. Alfred rescues him, using an anti-toxin developed by Fox. Crane later summons Rachel to Arkham and shows her that the toxin has been introduced into Gotham's water supply from Arkham for weeks, and then infects her. Batman confronts Crane, saves Rachel, and then takes her to his cave giving her vials for Gordon: one for inoculating himself and the other for mass production.

At Bruce's birthday celebration at Wayne Manor, he is confronted by Ducard, who reveals himself to be the real Ra's al Ghul, and has now arrived in Gotham personally to destroy the city; he had conspired with Crane to poison Gotham's water supply with the toxin, vaporizing it with a stolen device from Wayne Enterprises. After Bruce pretends to be drunk to get everyone to leave, he and Ra's fight. Ra's' men begin to burn down the mansion, release all the inmates at Arkham, and vaporize the hallucinogen into the atmosphere. Although Wayne Manor is destroyed, Bruce escapes the inferno with help from Alfred. Rachel delivers the antidote to Gordon and wards off Crane, now calling himself Scarecrow, with a taser. Batman reveals his identity to Rachel and then has Gordon drive the Batmobile to the central hub of the Gotham subway - Wayne Tower. Ra's boards the train; his objective is to send the water vaporizer on the train to a major water hub. As Batman confronts Ra's on the train, Gordon destroys the subway line. Batman jams the controls then escapes the train, leaving Ra's to die as the train crashes into Wayne Tower.

Following the battle, Batman becomes a public hero, and Bruce gains control of his company and fires Mr. Earle, the former CEO, and replaces him with Lucius Fox. However, Bruce is unable to hold onto Rachel, who, despite having fallen in love with Bruce, cannot reconcile with him as Batman. Gordon, now a Lieutenant, unveils a Bat-Signal and mentions a new criminal who leaves Joker playing cards at crime scenes. Batman promises to investigate, and disappears into the night.

Director Nolan said of Bale, "He has exactly the balance of darkness and light that we were looking for." Goyer stated that while some actors could play a great Bruce Wayne or a great Batman, Bale could portray both radically different personalities. Bale described the part as playing four characters: the raging Batman persona; the shallow playboy façade Bruce uses to ward off suspicion; the vengeful young man; and the older, angrier Bruce who is discovering his purpose in life. Bale's dislike of his costume, which heated up regularly, helped him get into a necessarily foul mood. He said, "Batman's meant to be fierce, and you become a beast in that suit, as Batman should be — not a man in a suit, but a different creature."

Since he had lost a great deal of weight in preparation for his role in The Machinist, Bale hired a personal trainer to help him gain 100 pounds (45 kg) in the span of only a couple of months to help him physically prepare for the role. He first went well over the weight required and created concern over whether he would look right for the part. Bale recognized that his large physique was not appropriate for Batman, who relies on speed and strategy. He lost the excess weight by the time filming began. The role of Bruce Wayne at age eight was portrayed by Gus Lewis.

Other cast members include Rutger Hauer as William Earle, the CEO of Wayne Enterprises who takes the company public in the long-term absence of Bruce Wayne; Mark Boone Junior as Gordon's corrupt partner Detective Arnold Flass; Ken Watanabe as Ra's al Ghul's decoy; Colin McFarlane as Police commissioner Gillian B. Loeb; Linus Roache and Sara Stewart as Thomas and Martha Wayne, Bruce's parents; Richard Brake as Joe Chill, the Waynes' killer; Gerard Murphy as the corrupt High Court Judge Faden; Tim Booth as Victor Zsasz; Rade Šerbedžija as a homeless man, who is the last person to meet Bruce when he leaves Gotham, and the first civilian to see Batman, and Andrew Pleavin as a uniformed policeman. Actors John Foo and Mark Strange appear as members of the League of Shadows Warriors.