After the Reagans worked together to put an end to the Blue Templar organization at the end of Season 1, Season 2 finds the family facing both personal and professional obstacles that are just as challenging. Frank ponders resignation after a high-profile lawyer and fundraiser for the Mayor-elect is found dead after seeing a prostitute. Jamie has his first undercover assignment at a local bar. Danny faces an Internal Affairs investigation. Finally, Erin must reopen an old rape case that Frank had worked on 18 years ago.
Cole Farragaut, a high profile lawyer and fund raiser for the Mayor-elect, Colson Poole, is found dead in his car under the Brooklyn Bridge. Danny and Jackie learn he had been seeing Nikolina, a prostitute, and was murdered in her apartment. From Nikolina’s interrogation, we learn that Cole started a fight with Nikolina’s pimp Kiril in an attempt to free her from Kiril’s employment. Lisa, Cole’s wife and college friend of Erin’s, asks that all of this information be kept from the press to protect her children. The Mayor-elect want to position it as a random act of violence to protect himself as he is associated with Cole. There is debate between Danny, Erin and Frank as to what is the right way to handle this situation. With Nikolina’s help, Danny and Jackie track down Kiril and to their surprise, Immigration and Customs Enforcement have Kiril deported to Croatia where there is an active warrant for his arrest thus avoiding any media exposure. Meanwhile Jamie has his first undercover assignment at a local bar where he "befriends” Noble, a popular drug dealer at the bar, who turns out to be part of the Cavazerre crime family. In addition, Frank submits his resignation letter to the Mayor-elect Poole, as is customary. By invitation from Poole, Frank and Erin attend a black tie fundraiser where Tony Bennett and Carrie Underwood perform. In the end Poole asks Frank to stay on as his police commissioner and he accepts.
Already having a bad day, Danny shows up at an inflated domestic dispute and gets into a screaming match with the couple. They are interrupted by a young man screaming for help who is being chased by a man with a gun. Danny and Jackie identify themselves as cops and yell for the perp to stop and drop his weapon but instead he continues running toward them, forcing Danny to shoot him. The man being chased continues to run away and they discover the badly injured perp is actually NYPD, Officer Tedesco. Per Frank, Danny is investigated by Internal Affairs like any other cop would be, which is debated at the Reagan Family dinner, and it is Danny who sticks up for Frank’s choice to go by the books. During this investigation Danny is on modified assignment and has turned in his gun and badge but he refuses to stop investigating the case. Eventually they track down the missing "victim” and learn that Officer Tedesco was hit hard on the head prior to the chase and due to this head injury he failed to follow protocol and identify himself to them as a cop. Danny’s suspension is revoked and he returns to full duty and he and Jackie track down and arrest the real culprits who attacked Tedesco.
Three men attempt to rob a bank, and after a customer shoots back, everyone escapes leaving one robber in the bank with two hostages including the shooter. One of the robbers is quickly found dead nearby while the other remains at large. Danny and Jackie, with Frank’s help, soon discover the identity of their bad guys and that the robber still in the bank is a former cop named Jimmy Flood, he was a Special Forces officer who had worked for Frank and had been fired because of his drinking problem. They also learn that Flood has an 8 year old daughter in the hospital in need of a heart transplant and this was his motive for robbing the bank. Danny goes into the bank to negotiate with Flood directly and is able to convince him to surrender. In addition, Danny and Jackie track down the other robber who had escaped. Meanwhile, Jamie works with a new partner Luisa, to do "Bingo Bags” in which they place a bag with a wallet and cash in it on a bench to catch people in the act of stealing and the two are at odds over the use of this tactic. At dinner, the Reagans discuss the Flood case, leaving them thinking about how far they would go in order to save their children.
Two teenagers have been murdered one seriously injured while playing basketball in the park, and although their parents insist they were good kids, Danny investigates into their lives to find out what led to the shooting. Working his way through possible motives he ultimately comes up with nothing. In the end he learns that in this case there is no mystery to solve, the victims were shot senselessly by a gang banger who misinterpreted an innocent comment one of the kid’s made as an insult. Meanwhile, Erin is assigned to re-open the case of Miles Thomas, a man who has been in prison for 17 years for rape, and Frank was the arresting officer. The arrest was completely viable at the time, and he was positively identified by the victim, however with advancements in DNA testing, it is now determined that his DNA does not match that of the rapist, who closely resembled Thomas. Thomas is let out of prison and now knowing who the actual rapist is but with no evidence to prosecute, Frank lets him know he is watching him closely. In addition, Jamie and Renzulli go undercover to investigate a stolen laptop and end up arresting the thief and the owner who turns out to be a bookie.
After a young man is killed in a staged accident which is part of an illegal insurance scam, Danny is determined to find justice. Upon investigating the clinic involved and doctor in charge of operation, Danny discovers that Rosalita, a parolee he knows is involved working at the clinic, and he enlists her to get the doctor to incriminate himself on tape. While Danny is conducting this investigation, he is also trying to have a romantic get away with Linda in the city for the weekend. In the end Rosalita gets the evidence Danny needs for the arrest and he and Linda get the quality time they needed. Meanwhile Jamie is invited by Nobel Sanfino to a party at his mob family’s restaurant and he goes undercover. Afterwards Nobel takes Jamie with him to torture the drug dealer who gave him bad drugs, and Jamie remains silent not wanting to blow his cover. In addition, Frank and Henry enjoy their weekend taking care of the boys while Linda and Danny are out of town.
The NYPD’s crackdown on subway fare-beaters draws the ire of Reverend Darnell Potter, a local African-American church leader, who accuses Frank of only targeting black neighborhoods. When Jamie and Renzulli enter his church on an armed robbery call, they’re assaulted by Potter’s security team and barred from entering. Frank is angered when Mayor Poole wants him to give special lenience to Potter, even as the reverend continues to stir up racial tension and play to the press. Meanwhile, Erin is surprised to find a smug former colleague, Lawrence Skolnick, is working a case against her, while Danny and Jackie determine the 911 call about the robbery was bogus and trace it to a drug dealer who says Potter made him do it. In order to escape drug charges, the dealer wiretaps Potter admitting to setting up the situation to draw publicity for his cause. When the recording is later leaked to the press, Potter, decides to step out of the limelight and Frank is redeemed.
Danny and Jackie investigate a serial killer who is targeting prostitutes. Despite Danny’s reluctance, Jackie goes undercover as bait to lure the killer. Jackie finds herself in danger when the serial killer turns out to be an unlikely suspect, and Danny must race to save her before she becomes the next victim. Meanwhile, Frank works with the union president to eliminate non-essential department spending, but the man proves unwilling to make concessions. While Henry organizes the Police Sports League, he runs into an old friend who offers him a job working at a private security consultant agency, but it turns out to be a ruse to gain the union better access to Frank. Erin hopes to deter Nicky from a law enforcement career by immersing her in the arts, but instead ends up on a date with the charming Jacob Krystal, an art appraiser who’s full of alluring secrets.
As the Reagans prepare for another Thanksgiving, Henry has a heart attack and is hospitalized following an emergency surgery. While the family worries over his recovery, Danny and Jackie investigate an East Indian girl’s death that hints at a forced suicide by her family, but later proves to be manslaughter committed by her white boyfriend, who was secretly dating the victim’s sister. Meanwhile, Erin learns from an NYPD detective that Jacob is an art thief, but after she confronts him, Jacob admits that he is involved in returning Jewish family heirlooms that were taken by the Nazis during WWII. Jamie learns that Renzulli owes his bookie three grand in gambling debt, so he borrows the money from his father, but Frank guesses who the money is actually for and advises Renzulli to clean up his act next time. Finally, a still recovering but indignant Henry wants to go home so he doesn’t miss Thanksgiving, but the Reagans wind up surprising him by bringing their holiday feast to Henry at the hospital.
After a convicted hit man agrees to give up information in several cold-case homicides in exchange for his son getting off on grand theft larceny charges, Danny and Sam Croft, Frank’s newly-appointed confidential investigator, escort the affable prisoner around New York to identify the locations where he dumped the bodies. The day proves successful until the convict’s hired thugs attempt to rescue him, which leaves Danny and Croft in a dangerous situation. Meanwhile, Jamie goes undercover in a boiler room run by the Sanfino crime family, but he winds up drawing the attentions of a beautiful former acquaintance and a dangerous gangster who suspects Jamie is up to no good. After Erin and Frank ask Croft to dig up info on Jacob, they learn that though Jacob’s past is suspicious, there’s not enough evidence to pin him to an art heist. However, Erin soon learns from Detective Deleon that Jacob has fled the country.
While building a racketeering case against construction contractors and union leaders, Erin is devastated to learn Ray Milo, her informant, is murdered by a hitman. As she speculates who outed him as a whistleblower and wanted him dead, Danny and Jackie investigate the two most likely suspects: a vengeful contractor, and a corrupt union leader who Milo planned to wiretap. After the hitman is arrested, Danny coerces him into revealing his employer is the contractor, who learned of Milo’s whistleblowing from the woman he was having an affair with: Milo’s wife. Meanwhile, Frank faces a media hailstorm after video surfaces online showing a NYPD officer assaulting an old man. But after obtaining the original, unedited video from the journalist who leaked it, Frank realizes the cop acted professionally and stands by the man’s actions.
Jackie and Danny investigate a cop shooting at a diner, but are surprised to find neither the cop nor the owner of the diner (Connie Markos) are still there. They eventually learn the cop is actually auxiliary police: a man named Mike Galatis who is Connie’s nephew. Connie was threatened by loan sharks and Mike killed Billy in self-defense. Although Mike swears Connie’s innocence, they find stolen handguns in Connie’s storage unit, and when Connie’s arrested, he puts the blame on Mike. Encouraged by Danny to do the right thing, Mike proves Connie’s criminality and this forces Connie to reveal the bad guy’s location. Meanwhile, the mayor wants to initiate a new NYPD recruiting campaign, Frank meets with Kevin Schmit, who wants him to exploit 9/11 and terrorism for the campaign. Inspired by Jamie, Frank instead proposes promoting the power of personal stories and connections that come from the job. Also, Jamie takes on a second job as a painter for Renzulli’s company because of his struggle to pay off his law school loans.
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 suspect. Meanwhile, Frank deals with the impending loss of a friend whom he worked alongside at Ground Zero. F. Murray Abraham ("Amadeus") guest stars.
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. Timothy Busfield guest stars.
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 assist in a sting operation to take down a narcotics dealer, but things quickly spiral out of control when one of the dealer’s associates, Phantom, kills an undercover detective. While the Reagans comfort the detective’s family, Danny becomes hell-bent on bringing his friend’s killer to justice. As Frank deals with the media attention, Linda and the boys worry about Danny. After Danny and Jackie learn that Phantom was a former drug kingpin now fresh out of prison, they track down Ray Bell, a former drug runner turned police informer. While Phantom holds Bell’s family hostage, Danny breaks in and kills Phantom after he refuses to give himself up. Later, the Reagans attend a talent show featuring Henry and Nicky.
When high-profile reporter and Frank's old flame, Melanie Maines, is almost assaulted while in town to investigate a controversial story, Danny and Jackie track down her would-be attacker to one of her cyberstalkers. But when the man's alibi checks out clean, Danny realizes that someone closer to Melanie, and carrying a grudge, could be behind the attack -- her own producer. Meanwhile, Jamie learns from Bianca Sanfino that Johnny Tesla is dead and whoever is behind the attack might try to lay it on Jamie. After Bianca goes off the grid, the Sanfinos confront Jamie and close in on him, but before things turn deadly, the cops stage Jamie's arrest and thus end his career as "Jimmy Riordan."
Erin prosecutes a woman accused of killing her rich husband, Samuel Delamar, but when the defendant’s attorney is suddenly murdered, Danny and Jackie’s investigation into the new crime might blow Erin’s whole case. Picking up where the slain attorney left off, Danny tracks down a mysterious man named Monroe and as a result, Danny is almost killed. While Erin’s witness, family friend Walter Harris, testifies that the couple repeatedly fought over Delamar’s money, Danny goes head-to-head with Erin in testimony by suggesting that Monroe, a shadowy business associate of Delamar’s, is very likely the killer. After Monroe is arrested, he admits killing the attorney to stop him from exposing his fraudulent dealings with Delamar but denies anything to do with Delamar’s murderIn the end, Danny and Erin learn from Monroe that Delamar was having an affair with Harris’ wife and that Harris killed him asa crime of passion. Meanwhile, Frank leads his own investigation into whoever is scamming his credit card, only to be put in an awkward situation when it appears an old friend is involved.
Frank is forced to lobby Reverend Potter’s (from #206) support for the NYPD’s gun buyback program, which follows one simple rule: bring your guns, no questions asked. However, when a gun linked to a robbery is brought in, Danny faces the dilemma over whether to arrest the suspect. He finally decides to bend the rules and coaxes the robber’s victim to make an ID of the man, only for it to turn out to be the wrong guy. When Frank learns of Danny’s actions, he is disappointed and urges him to start the case from scratch. Meanwhile, Nicky feels guilty for not sticking up for a friend at school and turns to Jamie for advice. Danny finally breaks the robber case when he uses his intuition to locate the actual suspect (who turns out to be the brother of the first man) and Danny is grateful to Frank for making him do things the right way.
Danny bumps heads in the department when he investigates a closed case, the suicide of a firefighter, at the behest of the man’s eleven-year-old son, who refuses to believe his father would kill himself. His perseverance pays off: Danny discovers it was not a suicide and that the firefighter was involved in a part-time construction business that was at the mercy of a corrupt building inspector taking bribes. Danny is able to connect the inspector to the murder, and the guilty man admits that after the firefighter refused to pay the bribe, they fought and the inspector accidentally killed him. Meanwhile, Jamie saves a baby from a burning building, only to stand in more danger of his undercover identity being blown by the press .In order to keep his cover, Frank asks Renzulli to publicly take credit for Jamie’s heroism.
During the murder trial of a notorious Russian mob boss, Erin’s key witness is killed by the mobster’s men, forcing Erin to turn to her only other eyewitness – a young Russian nanny. Danny and Jackie are assigned to protect the frightened girl, but after an attempt is made on her life, Danny realizes there’s a mob informant on the task force and he must uncover the rat. Danny is able to discover who the informant is and at the trial the mob boss tries to intimidate the nanny by threatening her family, but with Jackie’s help, the girl has the confidence to stand up and testify. Meanwhile, Mayor Poole offers Erin a position as deputy mayor, leaving Erin elated by the enormous opportunity and Frank conflicted. Caught between his job and Erin’s ambitions, Frank tries to avoid the tension with his daughter until it blows up into a confrontation over the competency of the NYPD. In the end, they make up and Erin decides not to take the job because she loves the one she has.
Danny and Jackie investigate the suspicious death of Phil Gibson, a high-rolling investor who sustained injuries in a fight, although his hands appear unmarked by trauma. After receiving an anonymous tip to investigate a nightclub, Danny learns that the investor was involved in a secret "fight club” boxing ring put on by Wall Street bankers. They learn that Gibson’s fight was part of an initiation process for all young employees with their bosses betting on the matches. Danny proves that Gibson’s boss is responsible, having doctored the gloves of his opponent in order to guarantee Gibson would lose his fight. Meanwhile, Frank forces Jamie under house arrest when the Sanfinos put out a hit on "Jimmy Riordan,” Jamie’s undercover identity, as well as Noble Sanfino. Wanting to warn Noble of the danger he’s in, Jamie confronts him with his true identity and offers him a plea bargain to testify against his family. He reluctantly agrees and Noble and his sister go into witness protection.
It is Mother’s Day weekend and Homeland Security informs Frank that the city is on high alert for a terrorist attack in the next 24 hours, the weapon is a biological flu virus with no vaccine. Frank and Mayor Poole disagree on how to handle the situation, Frank wanting to keep it quiet and not cause panic, and the Mayor wanting to go public. The mayor agrees to give Frank 6 hours to locate and detain the terrorists. Ultimately, through a routine traffic stop, The NYPD finds the terrorists and is able to prevent the attack. Meanwhile Danny and Jamie are at odds over a collar, a perp Danny identified to Jamie’s unit, and Jamie happened to see and arrest him. Once in custody, the perp Leo offers up information to Danny on a 2 year old cold case of his, a tip about a missing 4 year old boy that still haunts Danny. Leo’s information leads Danny and Jackie to a former garage attendant in the boy’s building who they discover also disappeared around the same time as the boy. By tracking the kidnapper’s mother on Mother’s Day they are led to his current whereabouts, and they discover he and his girlfriend have been raising the child as there own for the past two years. Danny and Jackie bring the boy home to his real mother alive and well. The Reagans sit down to their Sunday, Mother’s Day dinner and dote on Linda and Erin, and honor Mary’s memory as well.