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.
When a supporter for the mayor elect is found dead, Frank is put on the spot when the mayor wants him to position it to the public as a random act of violence. Meanwhile, Jamie goes undercover at a bar and meets a suspicious patron.
Jamie has his first confidence crisis when he fails, to mentor Renzulli's dismay, to draw his gun on a suspect who might have been armed and dangerous. Bored investigating a minor domestic row, Danny makes a split second decision to shoot an armed man, who turns out to be undercover colleague Lou Tedesco, hospitalized in critical condition, actually with a recent previous, mentally and physically crippling wound. Lou's apparent target, junkie Tyler Lee, and his friends and family prove key to the case. Danny is suspended pending an official IA investigation, but still...
Only one of four teenage schoolmates survives an apparently unprovoked shooting in a park. Danny has a hard time identifying suspects and working out a tragic motive. Modern DNA tests prove that a man whom the then inexperienced detective Frank Reagan got arrested as serial rapist was actually innocent. Despite the statute of limitations, the hunt for the real perpetrator is started.
Jamie is lightly hurt and sergeant Anthony Renzulli lands in hospital when they are abused, trying to respond to a fake robbery call, by burly 'security' hired by a ghetto church. Its 'reverend', Darnell Potter, is a provocative politician and a campaign friend of the new mayor. While Danny traces the fake caller and who hired him, chief Frank must resist press, public and the mayor, but financial scrutiny hands him leverage.
Grandpa Henry is approached by a fellow ex-NYPD-officer to consider the joining security firm Ajax Corporation, which is after police outsourcing contracts. To catch a serial 'escort' killer, Danny grudgingly guards partner Jackie, who insists on volunteering as bait since she physically resembles all victims.
Ayla Demir falls to her death within Jamie's reach. Her hot-tempered boyfriend Kyle Freelander's only alibi are his visiting parents. Her brother Hafiz firmly denies any suggestion of a honor crime as barbaric. Jamie discretely seeks help for his mentor's loan-shark problem. Henry Reagan's heart attack during Thanksgiving preparations ultimately only shifts the family spirit to hospital. Undercover FBI agent Anthony Deleon asks Erin's help against suitor Jacob Krystal, whom Interpol suspects for years of art robberies, for which he invokes an illegal excuse.
Danny accompanies a dangerous ex-mobster who is helping him find bodies on cold cases in exchange for leniency for his son on grand theft auto. Meanwhile, Jamie works undercover in a boiler room operation, looking for a secret about the Sanfino family.
A man who is a confidential informant working for Erin is killed. So she has Danny investigate to find out if he was killed because it was discovered he's an informant and if so how? And when a video that shows a police officer beating up someone comes out, Frank looks into it. First he talks to the officer who says that video was edited to make it appear he was rough on the man. He then learns that the source of the video is man who has it in for the NYPD and tries to get him to give the actual video.
On the way home with his family, Danny hits a man with his car who is fleeing from a gunman, and his family gets caught in the crossfire when Danny fires his weapon at the gunman. Frank deals with 9/11 guilt from impending loss of a friend whom he worked alongside at Ground Zero.
When a rich woman dies of a heart attack, her eccentric daughter claims that she received a message from God, who told her that her stepfather actually murdered her. Meanwhile, the archbishop wants Frank's support for the canonization of a local priest, but a reluctant Frank takes it upon himself to investigate a rumor that the priest went too far when protesting the Vietnam War.
When a man's family is robbed and beaten in front of him, and the assailant is shot and killed, the Reagan's debate about how far they would go to protect their family. Meanwhile, when a college student is arrested at a rally, Frank wrestles with her sentence due to her identity.
Danny and his partner survive an undercover operation to set up crack dealers, but friend Juan Cruz and his partner, whom they were in radio contact with, are shot by elusive rogue predator Phantom. Fear and misplaced loyalties complicate the investigation. Meanwhile Frank indulges in making the cop killer the ultimate priority and the family contemplates the plight of a constantly terrorized home front.
A TV journalist who has a "friends with benefits" relationship with Frank comes to town. And when she is nearly attacked but Frank saves her. He then asks Danny to investigate but she refuses to reveal what she is working on. So he speaks to to her producer who gives him a name of people who threaten her. And Jimmy gets a call from Bianca Sanfino who tells him that Johny Tesla is dead and her family thinks he did it because of what happened between them when JImmy was undercover. So he goes to see her and she is in fear of her life. He leaves but someone sees him and ...
As Erin prosecutes a woman accused of killing her husband, the defendant's attorney is murdered and Danny is assigned to the investigation. When Danny is put on the stand to be questioned, things get heated between the brother and sister.
Frank finds himself working with the Mayor and Reverend Potter from a previous episode, in a program to buy guns which may have been used in a crime but will not be used against them. But when a gun which was believed to have been used in a robbery wherein someone got shot, is turned in the officer who got it takes a photo of the one who turned it in and gives it to Danny. But Danny tries not to use it. But when he hits a road block; when the man who was shot was trying to describe the shooter to a sketch artist, Danny tries to lean him towards the man in the photo ...
Jamie rescues a child in burning building. The press are asking for the identity of the one who saved the child but because Jamie is still doing his undercover work, Frank tries to find a way for Jamie's identity not to be revealed. A boy whom Danny knows asks him to look into his father's death which was ruled a suicide. And Danny discovers a lot on inconsistencies.
Erin is prosecuting a murderous criminal. When her key witness breaks down when he was suppose to testify, Erin calms him down and schedules him to testify the following day, but he is killed, which means her whole case is dead. She speaks to someone who was there who claims to know nothing but Erin gets her to admit what she knows so she puts her in protective custody and Danny and Jackie are among the cops assigned to protect her. When they need something fixed they send for a repairman and when he arrives Danny senses something wrong about him and deduces he's a ...
Danny is investigating the death of a wall street guy and discovers an underground fight club. He learns that the man was drug which slowed him down and led to his eventual death. And Jamie has to choose whether to reveal to Noble Sanfino that he is a cop when he learns that there's a hit out on him.
It's Mother's Day. Frank learns of a possible attack using a biological weapon. The mayor wants to tell the people but Frank who doesn't want to alarm the people, wants to wait and see if it can be handled. Danny asks patrolmen to look out for a man he is looking for. Jimmy finds him and says it's his collar but Danny says it's his, which makes things tense between them.