Evidence against Danny surfaces when the attorney general's office reviews his shooting of a serial killer. Jamie and Eddie deal with a high-profile drunken driver. A slain cop's widow asks Frank for a favor.
Danny and Baez investigate the death of an elderly woman who was shot in her home by a stray bullet. Also, Frank faces ridicule from his department when he disciplines a disrespectful cop, and Erin steps in to help her detective, Anthony, find a legal solution to a case that’s personal to him,
A woman who was held hostage resists pressing charges, but Danny and Baez want justice for her. Meanwhile, a high-profile NYPD fund-raiser uses a phony police vehicle to avoid traffic; and Jamie has the opportunity to be a technical adviser on a TV show.
Intent on bringing justice to Lieutenant Gormley after he is beaten by a mob outside his home, Danny and Frank enlist the aid of Detective Anthony Abetemarco, who has a personal connection to the neighborhood where the attack occurred. Also, Eddie and Jamie witness a dishonest arrest, and Danny searches for a witness to testify against a dangerous gang leader
Erin and Anthony try to prevent the deportation of a prominent community activist who isn't a citizen. Frank must decide if the NYPD will participate in the U.S. Marshals' high-profile raid of a local gang.
A NYPD whistle-blower claims there's been abuse of power within the organization, so Frank must investigate whether this is true. Meanwhile, Danny and Baez are suspicious of a car accident involving a pedestrian and think it may have been intentional.
After Emily Harrison tells Danny and Baez she's concerned her abusive ex-boyfriend will repeat his behavior with his new girlfriend, Emily becomes the prime suspect when he's murdered. Also, Eddie gets jealous when Jamie lets a young woman crash at his apartment, and Frank must decide how to discipline a sergeant after he fails to intercede during an armed robbery while off duty,
Frank is left with minimal information to find a missing boy when a conflicted priest who could help won't break the seal of confession. Also, Danny and Baez investigate the death of a prominent New York City socialite with a secret life, and Jamie and Eddie attend a wedding together.
When the son of Frank's most outspoken critic in the African-American community, Reverend Darnell Potter (Ato Essandoh), is killed, Potter must put aside his contentious relationship with the Reagan family in order to get justice for his.
When Danny accepts a side job as a bodyguard for a recently released ex-con who took the fall for someone else, he uses the opportunity to go after the real criminal. Also, Gormley's wife, Sheila, asks Frank to give Gormley a bigger command position, and Jamie and Eddie witness a lovers' quarrel between two cops that leads them to reflect on their own complicated relationship.
When diplomatic immunity complicates a child abuse case for Danny and Baez, Frank intervenes, despite not having jurisdiction on the case. Also, a robbery occurs while Eddie and Jamie are on a double date with Eddie's boyfriend and his sister, and they are forced to step in.
While investigating the murder of a gang leader, Danny and Baez learn the accused shooter is an ex-con who is romantically linked to his parole officer, who might be assisting in a cover up. Also, concerned the murder might spark further violence, Frank steps in to mediate but must deal with Mario Hunt, the rival gang leader who killed a police chief two years ago.
While investigating the murder of a man who killed a mother and son years earlier while driving drunk, Danny and Baez are torn between doing their job and finding justice after discovering the connection between the suspect and the victim.
When Linda's brother, Jimmy (Kevin Dillon), gets into trouble with the mob, he begs Danny to help him stay safe until it blows over. Also, Frank faces a public relations nightmare when the lawyer of a wrongfully arrested man demands that NYPD records be made public.
Jamie and Eddie suspect foul play when they respond to a distress call from a woman having an allergic reaction to her lifesaving medication, and learn that her husband is an EMT assigned to take her call, but didn't respond. Also, Erin learns that a man she convicted years earlier might be innocent of the crime, and Frank handles a PR crisis in his department when an exposé on Garrett Moore is published.
An ex-NYPD officer goes missing the day after she reveals to Danny her plans to make amends to a woman she and her partner wrongfully convicted years ago; Frank faces a dilemma when one of his peers refuses to retire.
Erin faces off against her ex-husband in court when he represents the person she is attempting to convict of murder. Frank is confronted by a mother who accuses the NYPD of being negligent in solving her son's murder. Jamie rides with a new partner.
After Reggie Wilson, a witness in a former case of Erin's, asks her for help shutting down a drug operation in his apartment building, she makes it her mission to make the building safe for his family. Also, while investigating a teen's suicide, Danny and Baez uncover information that suggests the death was a homicide, and Frank looks into potential misconduct within the Mayor's office.
Danny and Baez team up with two Russian operatives to search for a dangerous Russian man who entered the U.S. on a diplomatic visa. Also, Frank gets involved in a sensitive case involving Archbishop Kevin Kearns.
In the season finale, when Danny intercepts a shipment of several million dollars that was heading to a drug cartel in Mexico, he becomes a target when they come back for revenge. Also, Jamie works independently to track down a serial killer who preys on the elderly.