Detective Caleb Evers tells partner Jarek Wysocki that gunshot victim Chris Collier (undercover officer Liam Hennessey) needs further surgery. Police superintendent Teresa Colvin had told Chris' family he was working undercover.
Jarek wonders if the grand jury will wait for Chris's testimony and how mobster Hugh Killian knew Chris was undercover. When Alderman Gibbons' choice for Colvin's chief of staff asks about Chris, Colvin smells the rat and arrests him on murder conspiracy charges.
Jarek tells Colvin that Chris said he wounded his shooter - Killian's daughter, Elizabeth - who must be visiting the mob's doctor, but can they tie this to Killian and Gibbons?
Meanwhile, Gibbons holds a press conference, citing rumors of Colvin being romantically involved with her murdered driver, Antonio. He asks her to resign to spare the city the expense of an investigation.
Colvin quotes Chicago newspaperman Mike Royko's observation that the city was built by men who demanded drunks and harlots be arrested while charging them rent - until the police arrived. But she refuses to comment on Gibbons' charges. The mayor tells Colvin that if her case against Gibbons fails, he'll accept the resignation she signed when she first took the job. Meanwhile, Jarek and Caleb locate and arrest Elizabeth.
Gibbons' aide Ellis tells him that Colvin gave Antonio's family checks they'll claim were hush money to cover their relationship, that "Liam" is alive, and Killian's now in a hotel, indicating he cut a deal to escape prosecution.
When Colvin asks Gibbons' assistant, Lily - who was arrested at the airport with $10,000 in cash - if she was sleeping with Gibbons, she refuses to answer, adding that she knows Colvin has no personal life, and leaves. Colvin then tells Killian about Elizabeth's arrest, and she asks FBI agent Kyler to approve Killian's post-testimony relocation.
Meanwhile, Jarek discovers his ex-fiancee, Elena, was arrested for DUI; she'd been drinking because she had just learned that her mother has weeks to live. He gets the charge dropped and promises to see her later. He also finds a photo of his dead brother, Vincent, with Killian on his desk.
When Jarek asks Gibbons about the photo, Gibbons says Killian killed Vincent. But Vincent's former handler tells Jarek that Vincent was investigating Russian gunrunners, not the Irish mob. And Jarek's father admits that Vincent told him that he'd done something bad, but he never told the police - or Jarek - this because he didn't want Vincent's name tarnished after his death.
Officers Vonda Wysocki and Isaac Joiner plan a romantic getaway while standing watch over Chris, who regains consciousness. Colvin rushes to his side, but Jarek interrupts their conversation to show her the photo. Jarek accuses Colvin of cutting a deal with a cop-killer, says he's leaving the investigation, and storms out.
Klyer tells Colvin that Killian's relocation's been approved, and asks her for a date. Colvin refuses, citing conflict of interest and the potential for scandal that could prevent any woman from holding her office in the future.
Jarek bursts into Killian's room, puts a gun to his head, and shows him the photo. Killian says that Vincent was a cop who'd given the Irish mob information about the Russians before telling the police - and took money for this. But he didn't kill Vincent and doesn't know who did. Caleb arrives, fakes a call from Killian to Jarek to cover the intrusion, and the detectives leave.
Meanwhile, Gibbons tells Lily that they can't have any further contact. She begs for his trust, promising to do anything for him.
Jarek and Caleb visit Vincent's former mistress Karen, who admits that she paid off her house with money that Vincent had stashed in a box there before he died. They find the box and half the money's still there - along with an old evidence tag.
As Kyler and Colvin enter the courthouse, Colvin spots Lily, who pulls a pistol, shoots Killian on sight, and gets arrested. Colvin tells Lily that Gibbons is the only person with enough clout to know when Killian would be arriving. Lily says that Gibbons is a great man and now she'll never be able to destroy him.
When Colvin tells Chris that Killian's dead, he says that Elizabeth can authenticate the mob's ledgers, so cut her a deal, because their main target is Gibbons. Elizabeth refuses until Colvin tells her that Gibbons ordered Lily to kill her father. While Elizabeth can show how the mob's money went to Gibbons, Colvin's afraid that's not enough to bring him down.
Jarek and Caleb match the tag to an evidence locker and find a videocassette on which Vincent claims to have information that will allow him to escape his compromised situation, but he gets interrupted by then-toddler Vonda, driving Jarek to tears. But Caleb discovers an envelope with Gibbons' name on it.
Jarek arrives at the mayor's office just before Colvin's resignation becomes official, saying that the envelope contains enough evidence for the grand jury to indict Gibbons. When Jarek tells his father and Vonda that evidence of Vincent's illegal activities will be used against Gibbons, his father orders him away. Vonda follows Jarek and, in tears, hugs him.
Gibbons asks his fellow aldermen to vote for Colvin's removal from office, which Colvin and Jarek interrupt with news of the grand jury's indictment - and Colvin handcuffs Gibbons.
As Chris reunites with his family, Vonda and Isaac plan their vacation, and Caleb parties with fellow officers. Meanwhile, Jarek visits Elena, Colvin comes on to a conventioneer in a hotel bar, and Gibbons sits in a cell - and smiles . . .