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The Reagan family races to stop deadly mayhem in the city when the gangs of New York unite to demand amnesty for the release of their imprisoned members and those awaiting trial.

After getting a match from an unknown relative from a DNA network, Sean Reagan does some detective work to figure out who this mystery person is; Frank gets a personal request from a woman (Bonnie Sommerville) to transfer her son to a safer assignment.

Danny and Baez investigate a series of drive-by shootings they think may be connected to six wrongly convicted men who were just released from prison.

In the conclusion of the two-part Season 5 finale, one of the Reagans is shot by a gang member, and Danny pursues a suspect while trying to keep his emotions in check. To add to the complications, Danny has to find an inventive way to bring in witnesses.

Jamie shares his suspicions with his family about Joe's killing and the now infamous Blue Templar. A private investigation leads them to the police officers who are the ring leaders of this secret group. Joe's death gets a fitting closure.

As Jamie and Eddie's wedding day approaches, Erin interviews a witness whose story leads her to doubt Eddie's honesty; Danny and Baez unravel the complicated love life of a young man who was murdered; Frank squabbles with the top brass.

The Reagans band together to prevent Joe Hill from being killed in the line of duty like his father when they fear Joe's cover has been blown within the gunrunning outfit he's helping the ATF bring down.

Shockwaves ripple through the Reagan family when Danny discovers that their newest family member, Joe Hill, is working undercover for the ATF to bring down a gunrunning organization.

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.

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.

Danny becomes the lead hostage negotiator when a prime informant in a large drug case holds Erin at gunpoint inside the courtroom.

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.

Jamie stands up for an officer who is harassed for testifying against her partner. Erin learns her lover may be her boss at the DA's office. Danny asks Erin to file murder charges against a man who shot a 15 year old girl who ended up dying 8 years later.

Danny Reagan is accused of police brutality. Frank has to walk a fine line in the investigation and find the truth. Jamie meets a female doctor, and it makes Janko uneasy.

After someone breaks into Luis Delgado's home and kills his wife, Luis and Danny team up to take down the vicious murderer who may also be responsible for Linda's death; Frank finally meets Eddie's mother; Jamie and Erin are at odds.

Danny and Baez work with Texas Ranger Waylon Gates when they are part on a case to find the Lone Star Killer; after Eddie's partner mistakenly shoots an undercover cop, Internal Affairs accuses Jamie of not supervising properly.

Danny gets himself into trouble after being told not to pursue a suicide case of a C.I. of the D.A. Jamie and Janko get involved in an immigration case of couple wanting to get married, but the bride's father is against them.

A woman's abusive boyfriend targets Jamie after he intercedes in a domestic dispute. Elsewhere, the press get ahold of an illegal tape capturing Henry's insensitive comments, and Frank must deal with the ensuing scandal.

When the son of Frank's most outspoken critic is murdered, Frank and the boy's father must put aside their differences to seek justice.

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.

Jamie and Joe search for an undocumented teenage girl who has been sex-trafficked; a woman in witness protection is murdered; Frank calls out the district attorney's office for instituting a new rule.

Danny is pulled over by a cop who asks if he can look what he has in the back of his vehicle. Danny asks him what's going on, he says he got a tip that a vehicle like the one Danny is using, was at a drug buy. Danny thinking it's outrageous and lets him look but the cop finds some drugs and arrests Danny. When the family learns of this, Linda wants Frank to intervene and he doesn't think he should and he says that's for everyone. Henry asks Erin's ex to defend Danny and he does by making him question his trust of his partner. And when he sees her with the IAB Captain investigating him, he wonders if he can trust her.

When NYPD Deputy Chief Donald Kent and his wife are gunned down in an apparent gang hit, Frank orders the whole department to scour the city for his friend's killer.

Danny and Baez race to find a girl who will die without her medication; Jamie and Eddie are on the wrong side of an investigation after engaging in a car chase; Sean wins an essay contest.

The drug cartel hitman responsible for torching Danny's house resurfaces. Also, an attack on an officer in the line of duty directly impacts a member of Frank's team; Eddie reluctantly introduces Jamie to her mother, Lena; and Erin deals with the consequences of her new role as boss.