Frank is put on the spot when a supporter for the mayor is found dead and the mayor wants Frank to position it as a random act of violence to the public. Meanwhile, Jamie goes on his first undercover assignment at a bar where meets and bonds with a suspicious patron.
When Danny is put on modified assignment after an incident in which a cop--who failed to identify himself--is shot, he faces Internal Affairs investigators, who are looking to his state of mind on that day for further implications.
Three men attempt to rob a bank and Danny discovers that one of attempted robbers is a former cop. Also, Jamie works with Luisa Sosa, his new partner.
Erin has to re-open a 18yr old rape case in which Frank was the arresting officer. Danny and Jackie have to deal with the murder of three teenagers for which there appears to be no motive.
Even while on a case, Danny tries to swing a romantic weekend with Linda. Jamie's undercover assignment involves a crime family.
Frank deals with a political crisis after Jamie and Renzulli are injured by a church security team that refuses to let them enter a religious center in response to a 911 call.
Jackie goes undercover as an escort when she and Danny track down a serial killer who is murdering prostitutes in hotel rooms. Meanwhile, Erin meets a potential suitor at an art gallery who shares her interests.
Henry's heart attack on Thanksgiving eve leaves the family contemplating a future without him. While Danny and Jackie look into a suicide that may not be what it seems, Frank and the mayor disagree about a threat to the city.
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.
When Erin's informant is murdered, she blames herself and works to help Danny discover who killed him.
Danny and Jackie investigate a murder scene at a diner, where a witness claims a uniformed officer fled the scene after shots were fired.
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 Jackie investigate the murder of a Reagan family friend who was an undercover detective. Danny's family starts to worry as the persistent search takes an emotional toll on him.
When Frank’s close friend, a high-profile reporter, is almost assaulted while in town investigating a story, Danny and Jackie attempt to track down her would-be attacker. Meanwhile, Jamie’s undercover case comes to a head.
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.
Danny is put in a difficult position when a gun linked to a robbery is brought in to the NYPD’s gun buyback program. He must decide to either arrest the suspect or follow the no questions asked rule.
Danny causes waves in the department when he investigates a closed case, the suicide of a firefighter, at the insistence of the man’s 12-year-old son. Meanwhile, Jamie saves a baby from a burning building but worries it will jeopardize his undercover work when he is billed a hero in the press.
Danny and Jackie are assigned to protect a key witness in a Russian mob trial, but when an attempt is made on her life, they realize there is a leak on the task force. Meanwhile, Erin is offered a job as deputy mayor, which would have her working directly with her father.
Danny and Jackie investigate the suspicious murder of a high rolling investor, who had injuries from a fight, but no marks on his hands. Meanwhile, Frank puts Jamie under house arrest, when the Sanfino family put out a hit on "Jimmy Reardon".
Frank must race to stop a biological weapon attack on New York City, while keeping it a secret from his family during their most sentimental holiday, Mother’s Day. Meanwhile, a long-standing conflict between Danny and Jamie comes to a head.