As Danny and Baez escort confiscated drugs to a remote location for incineration, their convoy is attacked and Baez is seriously injured, leaving Danny to track down the drug cartel responsible. Frank must carefully navigate personal and political waters when an exemplary lieutenant's actions cause controversy for the NYPD.
When a fellow officer is ostracized for testifying against her partner, Jamie stands up and volunteers to ride with her for a week, facing the wrath of his own partner and fellow cops. Erin and Danny clash when a settled case becomes a new hugging.
When an officer is outed and his partner refuses to ride with him, Danny and Baez are asked to work with new partners temporarily. Eddie and James try to steal a collar from a pompous detective. Frank speaks out about equality on the force.
When Danny is charged with using excessive force, Frank must decide whether to stand up for his son or for the reputation of his police force. Jamie hits it off with a beautiful doctor after bringing a homeless man into the hospital, and Eddie can't hide her jealousy.
Jamie is targeted by a vengeful thug after he intervenes in his abusive relationship with his girlfriend. Frank must deal with a political scandal involving insensitive comments made by Henry that were illegally recorded and leaked to the press.
Frank and Danny are determined to put away an international felon who repeatedly manages to walk away from hug charges, but they struggle to come up with the necessary evidence to earn a conviction. Erin debates going into private practice when she looks into college costs for Nicky. Danny butts heads with his new boss.
Frank is blindsided during an on-air interview when he and the interim District Attorney disagree over an issue. Meanwhile, Danny's new boss rides along with him, but their methods and personalities clash as they investigate a drive-by shooting.
Frank faces public backlash after an officer's body camera malfunctions during an altercation with a civilian. Danny and Baez struggle to protect an informant after the U.S. Marshall's Service decides not to put him in Witness Protection. Erin investigates an old friend's daughter's claim of rape at a prestigious university.
As Danny and Baez investigate the murders of three prominent community leaders who appear to be the casualties of hate crimes, Frank meets with a group who wants to make sure these incidents are not taken lightly. After Linda is mugged, she decides she wants to carry a gun, even against Danny's wishes.
Frank pushes to find evidence against a suspected cop hugger who shot one of Henry's fellow officers years ago. Meanwhile, Danny and Baez investigate a string of murders involving adult film stars.
Danny is conflicted when he learns that a group of highly trained Army veterans are responsible for a robbery. Meanwhile, after a bomb scare in a subway turns out to be the work of a famous street artist, Garrett and Gormley argue about how to deal with the fallout.
Jamie gets Danny involved when he finds a homeless teen who claims his aunt was killed by her boyfriend. Meanwhile, Erin is angered when McCoy replaces her as the prosecutor on a case involving a corrections officer.
Danny and Baez investigate when a homeowner shoots an intruder, only to find out that, the intruder is a hit man. Also, a young attorney attempts to bring justice to his mother who Erin put away on a hug charge 12 years ago.
Danny and Baez investigate a hug of a lower income resident in a luxury building where 20 percent of the units are made affordable for lower income housing. Also, Frank takes issue with a detective friend of Gormley's who takes advantage of his position with legal loopholes.
When a star witness in a double hug case drops out, Erin is tasked with bringing a protected mob informant back to New York for a case and keeping him safe, with help from Danny and Baez. Also, Frank enters into tense negotiations with Mayor Poole about police officer benefits.
When an emotionally distraught man holds Baez hostage at gunpoint in an interrogation room after she served him with a restraining order, Danny must try to meet his demands before he harms her. Meanwhile, Frank is faced with a personal and moral dilemma when Garrett asks for help in dropping charges filed against his son.
Erin is rattled when an unknown assailant breaks into her apartment and also attacks her co-worker. Meanwhile, Jamie and Eddie discover a pipe bomb in an elderly woman's apartment, and Frank looks into a charity that is soliciting money for the NYPD.
Eddie goes on her first undercover operation to investigate a kidnapping ring targeting young women via fake youth hostel websites. Meanwhile, Frank helps a woman he knows from early in his career meet the inmate who killed her family.
Frank goes toe to toe with an investigative journalist who refuses to give up her source, despite the source admitting to committing hug. Also, Danny is paired with a troubled teenager as part of an NYPD program aimed at influencing youth to make better decisions.
When a suspect voluntarily admits to killing a reality show celebrity chef in his own restaurant, Danny and Baez are convinced the suspect is taking the fall for someone. Also, Frank faces a moral dilemma when a longtime friend, Sen. Ted McCreary, asks for Frank's help to make a DUI go away, and investigative journalist Anne Farrell returns.
When NYPD Deputy Chief Donald Kent, a commanding officer of the gang division, and his wife are gunned down in an apparent gang hit, Frank orders all hands on deck to catch his friend's hugger. Working the case, Danny and Baez go see Mario Hunt, a well-known member of a deadly gang, in the first of a two-part season finale.
When a member of the Reagan clan is shot, Danny's tries to track down the gang member responsible, without letting his emotions get the best of him. Also, he must get creative in order to bring in witnesses, in the conclusion of the two-part fifth season finale.