A married, family man and supporter of the new Mayor, involved with a Croatian girl, is shot dead. The Mayor is averse to bad press. Frank stays on as Commissioner. Plain-clothed Jamie unknowingly helps a mob member who had over-dosed.

Frank deals with a political crisis after Jamie and Renzulli enter a religious center in response to a 911 call and are injured by the church's security team who prohibits them from entering.

A girl falls from her apartment window and dies. Danny investigates. Henry has a heart attack and spends Thanksgiving in the hospital. Tony gets cash to square off his gambling debt, with a warning from the Commissioner.

Nicky gets a reality check when her absent father shrugs her off. An illegal immigrant is robbed of his cash. His son accidentally kills the robber. Danny coaches the son in making a statement which would get him a lower sentence.

A reverend, the mayor and the police organize a gun buyback plan, with no questions asked. There, a gun used in a shooting at a chemist's is traded in. Danny investigates without being able to use the evidence from the buyback program.

Erin's witness in the murder trial of a violent mobster is killed before giving testimony. Due to a leak, the next witness is threatened, but protected by Danny and Jack. Erin is offered the Deputy Mayor's position, but she declines.

The police come to know of a citywide biological threat and Frank deals with it. Danny, hunting for a petty thief, gets a tip which helps resolve one of his unsolved cases. Jamie and Danny argue about booking rights for this petty thief.

When two motorists driving gas-guzzling cars die at the hands of a sniper, Danny and Kate are put on the case of what the city believes is the work of a radical environmental serial killer.

Jamie must deal with the emotional consequences of his actions on the job. Susie Essman and Annabella Sciorra guest star.

When a man with multiple rat bites is thrown from a moving car, Danny works the case to find out why and who was trying to send a message. Mary Elizabeth Mastrantonio and Mark Moses guest star.

Danny gets a call to go to a project where a gang rules with fear and intimidation. Jamie finds a girl standing on the roof holding her baby, saying she can't stand their lives being controlled by street gang Los Lordes so she jumps to death with her baby. Danny later learns that the girl was someone he met when she was younger when her parents died and he said he would help her and her sister. Danny goes to her sister who is bitter that Danny forgot about them. He learns that she is now with the leader of the gang. While Jamie and his partner are walking through the project there's some shooting and Jamie's partner is hit. Frank later learns that the D.A. is not pressing to prosecute the gang so Frank goes to the mayor for help.

As the Reagans rally together to take down the leader of the gang responsible for the murder of someone close to them, Danny looks to the gang leader's girlfriend to lead them to him.

When an officer is accused of using excessive force on a suspect, Frank finds his department under scrutiny from the community and the mayor.

Danny's loyalty is tested when he is assigned to the case of a childhood friend, Mickey, who is under investigation for having ties to an infamous mob family. Meanwhile, Frank gets word that crime is on the rise due to a recent judicial ruling about the legality of the "stop and frisk" policy.

Baez gets injured while escorting confiscated drugs, so Danny goes after the drug cartel responsible. Elsewhere, a lieutenant with a commendable record engages in controversial behavior, putting Frank in a difficult situation.

A mob informant returns to the city to testify in a case for Erin, and Danny and Baez are tasked with protecting him. Elsewhere, Frank and Mayor Poole get into heated negotiations regarding benefits for police officers.

A possible serial-killer case is assigned to Danny and Baez. Erin considers becoming a judge; a mayoral candidate claims that Frank has been secretly investigating her spouse; and Eddie confronts her dad.

Erin is overwhelmed with guilt after a man she set free is accused of killing a cop. Also, Frank and Mayor Poole continue their game of political chicken over Frank's reappointment as commissioner, and Danny and Maria investigate a case of a cop who has gone AWOL.

In the Season 6 finale, public outrage erupts when a cop isn't indicted for shooting a teenager, and the fallout affects Frank, the mayor and Erin's office. Later, an officer gets shot in a possible case of retaliation, so Danny searches for the shooter.

A Mexican drug cartel targets Danny when he intercepts a shipment of several million dollars; Jaime goes after a serial killer who preys on the elderly; Mayor Poole confides in Frank that he plans to retire.