The film opens in 1933 as John Dillinger (Johnny Depp) is brought to a penitentiary by his partner John "Red" Hamilton, under the disguise of a prisoner drop. They are actually there to break out the rest of their gang. Dillinger and Hamilton overpower several guards and free their partners. After a gangmember gets violent, a gun is used to kill a guard alerting the rest of the prison. A shootout ensues as the gang makes a run for the getaway car. This results in Dillinger's mentor Walter Dietrich being killed. After beating and disposing of the gangmember who caused the shootout, Dillinger and the gang take refuge in a country house before leaving for Chicago to rob banks.
Elsewhere, Melvin Purvis (Christian Bale) and several other FBI agents are running down Pretty Boy Floyd. Purvis kills Floyd, and as a result, Purvis is upgraded by (J. Edgar Hoover), who is protecting the FBI from scrutiny by politicians, to lead the hunt for John Dillinger.
While Dillinger and his gang reap the benefits of their robberies, Alvin Karpis offers Dillinger a role in a kidnapping plot. He declines however, stating that the public doesn't like kidnappings. At the party he meets Billie Frechette, whom he takes to dinner. At the restaurant they are in, they both are looked upon by others; John with fear because they know who he is, Billie with disdain because of her Native American heritage. Billie leaves him at the restaurant however when John begins talking to associates of Frank Nitti, Al Capone's right hand man and confidant. He finds her later, and states plainly that she's his girl now and that he will do anything for her: he also stands up for her by beating a drunk verbally abusing her. With this act, and impressed by his respect and straight-forwardness with her, Billie leaves with him.
Melvin Purvis gets a lead on where Dillinger is staying and sets up an ambush at the motel he believes he is in. While checking out "Dillinger's" room, Purvis finds what looks to be an ordinary husband and wife. Though their identification checks out, Purvis seems to recognize the husband and has an agent watch the door after he leaves. But when the agent sees someone approach the door he is ambushed and killed by the "husband". After the man escapes, due to the rest of the agents' incompetence, Purvis realizes the killer wasn't Dillinger but Baby Face Nelson. After this incident, Purvis demands that Hoover bring in professional lawmen who know how to catch criminals dead or alive. Though Hoover had hoped for more pristine agents, he agrees.
While he and Billie are enjoying the luxuries across the States, the police finally find Dillinger and arrest him and his gang in Tuscon. In prison, Melvin Purvis comes to meet Dillinger. Dillinger goes on to tell Purvis how killing is different up close and personal as opposed to the way he killed Pretty Boy Floyd. Purvis tells Dillinger that he will more than likely be executed, and won't be a problem much longer. He is soon taken back to Indiana where he is imprisoned awaiting trial. The prosecutor wants to house Dillinger in the state prison; Dillinger's lawyer convinces the Judge to keep him in the county jail. Before trial, Dillinger and a few inmates escape using a fake gun. Dillinger is unable to see Billie as she is under tight surveillance by Purvis' men. Soon he finds that Frank Nitti's Chicago Outfit associates are now unwilling to help him; Dillinger's crimes are motivating the US government to begin prosecuting interstate crime, which imperils Nitti's (and others') lucrative business as bookmaking.