Detective Jarek Wysocki is having a recurring nightmare. Chasing a suspect though the old Cabrini-Green projects, he fires three shots, but the bullets bounce off. The suspect laughs, shoots, and Jarek - in bed with his ex-wife, Deena - is awakened by a 3 a.m. phone call. As Jarek leaves, he's confronted by his son, A.J., who realizes that his parents are still sleeping together. They plan to discuss this later.
Police superintendent Teresa Colvin tells Jarek and his partner, Caleb Evans, that armed men were spotted loading a yacht in the harbor and major heroin dealer Daniel Romero is aboard. She wants Jarek to bust Romero during the money/drugs exchange.
As Jarek and Caleb lead the raid, Romero runs and is captured. But no drugs - just cash and guns - are found at the scene, so they can only hold Romero for 48 hours.
Meanwhile, undercover officer Liam Hennessey is having nightmares about his recent arson job resulting in an accidental murder. He's interrupted by an Irish thug bringing Liam his cut from that job - and a summons to Alderman Gibbons' office.
Liam goes to the station and forces a confrontation with Jarek so they can speak privately. Liam is having second thoughts about working undercover. Jarek tells him to man up.
Colvin tells Jarek that the FBI wants to question Romero, but Jarek wants to shut down Romero's local operation before handing him to the feds. Meanwhile, Caleb overhears Romero's wife, Beatrice - waiting outside with his brother, Lucho - tearfully praying for her son.
Jarek and Caleb tell Beatrice that Romero told them about their son. Beatrice reveals his name, Marco, and that he's being held for ransom, before discovering their ruse and exiting. Jarek realizes that the found cash was ransom money.
As Gibbons explains his visiting the bereaved family of every dead constituent is more than politically motivated - it's about compassion and ritual - he welcomes Liam into his office. Gibbons says that his regular driver is off today, and asks Liam to fill in for him.
When Jarek and Caleb offer to help Romero by capturing the kidnappers, Romero replies that they only want to force the kidnappers to inform on him, adding he'll deal with the kidnappers when he's released. Jarek is interrupted by Deena, who wants to get their story straight before talking to A.J. Then Caleb gets a call on Romero's cell phone that details when and where the new ransom deal will go down.
Meanwhile, Gibbons wants Liam at his side while comforting the first bereaved family on his list. Afterward, Gibbons, noting Liam's discomfort, gives him a silver-tongued lecture about being self-centered.
Colvin tells the FBI that Romero's caller - unaware that he's in jail - had a Nigerian accent. She wants Romero to comply with the demands, so that they can bust his Nigerian drug rivals - and protect his seven-year-old son. After speaking with his lawyer, Romero agrees to do this while wearing a wire and a bulletproof vest.
When the FBI demands Romero be handed over immediately, saying his RICO charge trumps any local case, Jarek enlists Vonda and Isaac - currently on lock-up duty as punishment for Vonda taking the fall on that botched frisk last week - to give the FBI a different prisoner, which they blame on a mistake in the paperwork.
Meanwhile, Jarek and Caleb arrive at the exchange point. Jarek spots two men on a rooftop and sends Caleb and another officer after them. Then the Nigerians roll up, but Marco is nowhere in sight.
Taken by surprise, the rooftop men open fire as do the Nigerians. Caleb and the officer overpower the rooftop gunmen, who turn out to be members of Romero's gang. Romero's wounded - the bulletproof vest saved him - and all the criminals are arrested, but Marco is still missing. Jarek thinks that Romero used his lawyer to tip off his gang.
While the FBI wants to place Romero in the witness protection program, Jarek and Caleb confront Lucho - whose number appeared on the Nigerians' cell phones - and threaten to tell Romero about his role in the kidnapping unless Lucho reveals Marco's location. When he does, police raid the place, and Jarek rescues Marco.
After reuniting Romero and Marco, Jarek and Caleb note that while Lucho will testify against Romero, the feds will cut Romero a deal in the RICO case, so he'll walk. But Jarek says that he's got one more card to play, which involves Colvin persuading the FBI to place Romero's wife and son into witness protection in return for Romero's testimony and a life sentence. To ensure his wife and son's safety, Romero agrees, and they all have a teary-eyed farewell.
Meanwhile, Gibbons' next stop brings Liam face-to-face with the widow of the man he accidentally killed, which visibly upsets Liam. Back at the alderman's office, Gibbons addresses Liam's concern, saying either you want to be part of our organization or you don't. Liam says he does.
Liam then meets with Colvin, noting that Gibbons is holding that arson/murder over him, and he vows to bring him down.
Jarek and Deena try to explain their relationship to A.J., and Deena realizes Jarek's incapable of choosing between her and his fiancee, Elena. She tells Jarek that she's going to start dating someone else. Jarek heads for Elena's, kisses her goodnight, and stares out the window.