Malone is targeted for murder by two gangland factions just as he reaches a decision to dramatically change his life. Disguised as priests, two gangsters burst in on an Irish communion breakfast to kill bootlegger Pauly Gaughan, slaying several children in the process. Sure that Capone is responsible, a rage-crazed Malone violently interrogates Vito Stellini, and is about to kill the gangster when Ness stops him. Stellini tells Capone what happened, and all agree that Malone is becoming a major problem. Later, Ness attends the wake for one of the slain children, where his father, Coffee Ryan, announces plans to kill the men who killed his son. Ness puts Ryan under surveillance, but realizes Malone poses a bigger threat. He finds his friend in a speakeasy, drunkenly threatening Capone and his cohorts. Later that night, Malone is assaulted and brutally beaten by four anonymous men, only to be saved from death by an Italian widow.
While transporting a teenaged prisoner, Ness learns how unfair the system can sometimes be when he finds out the truth about the boy's crime. When gangster Jasper Mullins guns down Al Capone's favorite bag man, the mob boss vows revenge. So Eliot Ness is less than thrilled when he learns that he and Quinlan have been assigned the task of transporting Mullins to trial in Indiana. Then, at the last minute, Mullins comes down with appendicitis, leaving Ness and Quinlan with transporting a teenaged convict named Cornelius Tucker, who has been sentenced to serve twelve years in federal prison. Of course, Capone's men don't know about the change, so when Frankie Rio joins with hit man Johnnie Peters to kill Mullins, his instructions are to seek out a car driven by Ness.
The Capone ""family"" loyalty is tested when Frankie Rio's younger brother blows his cool and kills a member of a rival gang. Capone and his men are infuriated when police raid a party honoring Frankie Rio's mother's sixtieth birthday. The cops later apologize, explaining that they were given an anonymous tip that the party was actually the site of a secret arms deal. When the capos learn that rival gangster Aldo Genna provided that tip, Frankie's hot-headed younger brother, Johnnie, tracks Aldo to a restaurant and guns him down, killing an innocent waiter and wounding AIdo's brother, Mike Genna, in the process. The only person to see Johnnie's face is a restaurant patron, Professor Milton Revis, who rushes out in fear for his life.
The brutal murder of an old friend and his own son's serious illness force Al Capone to re-evaluate his life of crime. While his son lies ill with a serious fever, Al Capone attends a farewell dinner with Carmine Maggi, an old friend who is leaving Chicago and the Mob to start a new life. Maggi encourages Capone to get out of the crime game, and Capone, worried about his son and his family, is moved by his words. Capone leaves the table for a moment, and returns to find Maggi dead from machine gun fire, then realizes that he was probably the intended target. Ness has Capone subpoenaed and questions him, but is convinced the mobster had nothing to do with the murder. However, since Capone was at the scene, he orders him to stay in Chicago.
Ness falls for a beautiful call girl while investigating a blackmail racket linking Capone to several noted court judges. The night before he is scheduled to appear before a judicial review board, Judge Ryan is found on the street below his luxury hotel room, the victim of an apparent suicide. Although a note is found in the judge's pocket, Ness and the Untouchables are suspicious. They learn that the judge spent his last night in the company of a young woman named Sybil, a model who works for CIeo Paine, whose agency is rumored to double as a high-class call-girl operation. Since every judge that is associated with a Capone case has been spotted with one of CIeo's models, Ness can't help but wonder if there is a connection and sets up a round-the-clock surveillance of CIeo's apartment. Watching Cleo from across the street, the just-divorced Ness can't help being struck by her beauty
Untouchable Paul Robbins takes on the Old West when he travels to a frontier town to bring back a captured Capone thug. Enraged by a string of losses to other gangs, Capone jumps on the opportunity to exact revenge on a rival. He puts Frankie Rio in charge of the counterattack, but Rio is unable to locate any of his regular thugs. Instead, he calls on two friends, July Manetti and Mel ""the Mute"" Lugar. They successfully gun down gangster Vic Mancini, but a witness sees the shooting, and Untouchables Robbins and Pagano are sent to arrest the thugs. Unfortunately, during the attempt, Pagano is shot and seriously wounded. Certain the Untouchables won't rest until they catch the shooters, Rio helps his friends escape on a train to San Francisco.
Robbins defies Ness's orders and investigates Capone's connection to a plan to take over Chicago's railroads. Pressured by Bureau of Investigation agent E.Q. Johnson, Robbins tries to convince Ness to look into the mysterious murder of two railroad police. Ness refuses, unwilling to get involved with the Bureau or to divert attention from Capone's expansion into Florida. Ironically, Nitti is also interested in the railroads, and has no more luck convincing Capone to listen. Convinced he is on to a sure-fire scheme, Nitti goes behind Capone's back and teams with a hood named Drenik to pay Lewis, a shady foreman, to run for head of the railroad workers' union.
While investigating the robbery of one of Capone's banks, Ness finds himself drawn to the Indian who committed the crime. A group of Indians led by John Littlehorse rob a bank owned by Al Capone, inadvertently stealing bills that the Untouchables had marked in an attempt to link Capone to his illegitimate dealings. Realizing this could be the key to nailing the mobster, Ness and his team immediately make plans to track down the Indians. Capone is also compelled to retrieve the cash, afraid of losing the upcoming Florida deal if his prospective partners learn of his connection to any ""dirty"" money.