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 and Baez are temporarily assigned new partners when an officer is outed and his current partner won't ride with him. Meanwhile, Jamie and Eddie work on a revenge mission to steal a collar from a pompous detective, and Frank compromises his relationship with the Archdiocese when he speaks out about equality in the police force.
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.
Frank is taken by surprise during an on-air interview with Erin's boss; Danny and his new boss clash as they investigate a drive-by shooting. Meanwhile, Jamie and Jenko help out detectives with an apparent suicide.
Three community leaders are killed in apparent hate crimes, and Danny and Baez investigate as Frank meets with folks who want to ensure the gravity of these crimes is not ignored. Meanwhile, Linda wants to protect herself with a gun after getting mugged.
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.
Danny and Baez look into the murder of a lower income resident living in a luxury building where a percentage of units are available for lower income housing. Frank disagrees with a detective friend of Gormleys.
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.
Baez is held hostage in an interrogation room by a distressed man who wants to see his daughter. Elsewhere, Garrett's son gets in trouble with the law, so Garrett turns to Frank for help, creating an ethical dilemma for the police commissioner.
Erin's unnerved when someone breaks into her apartment, and then she discovers her coworker was attacked. Elsewhere, Jamie and Eddie find a pipe bomb in a senior citizen's home; and Frank investigates a charity that's supposedly helping the NYPD.
Eddie goes undercover for the first time when she tries to take down a kidnapping ring, which is luring in young women with websites for phony youth hostels. Elsewhere, Frank assists a woman who wants to confront the inmate who murdered her family.
A celebrity chef from reality TV is murdered and a suspect readily confesses to the crime, but Danny and Baez think there is more to the case. Jamie and Jenko investigate a bizzare assault and elsewhere a senator uses his friendship with Frank to ask for a favor regarding a DUI charge.
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.