Elias is talking on the phone, wondering what kind of man he would have been if his mother hadn’t been murdered.
Carter is seeing her son Taylor off to school and realizes that he’s upset about something. He explains that some rich student is giving him trouble because he’s there on a scholarship, but insists on handling it herself. Taylor tells his mother that he’ll catch the subway home that night because she’s working. As Carter watches her son go inside, she gets a call from Detective Sherri Lablanca in SID. She tells Carter that the accounts that Elias used for his recent investment scam have been drained dry.
Reese arrives at the library and Finch tells him that they have five numbers: the five heads of the New York mobs, including Gianni Moretti Jr., who took over when his father went to prison. They figure that the only person crazy enough to take on the mob leaders is Elias, who has already kidnapped his father and plans to take control. The five Dons meet at the Covenant Club in Brooklyn, and Finch goes in and hacks the fire alarm system sound system.
The two men listen in as four of the mobsters discuss the usual business. Gianni Jr. wonders when they’re going to retaliate against Elias. However, the other mobsters are willing to let it go, figuring that Gianni Sr. set himself up by killing his wife, Elias’ mother. As long as Elias brings in money, they don’t care what he does. Finch figures that they need to convince the mobsters won’t make a deal, and tells Reese to call and apologize to Carter so she’ll start working with them again. Reese makes the call but Carter ignores it. She’s meeting with Lablanca, who says that Elias shipped the $4 million out to a thousand payees as cash and wire transfers, making it impossible to trace without months of effort. As Fusco secretly listens in, Carter figures that Elias is using the money to make pay for a lot of bribes.
Elias goes to the winery where he's holding the imprisoned Gianni Sr. and brings him some food, but refuses to leave him a knife. He tells his father that Gianni and his ilk have gone soft, and Gianni wonders why he doesn’t kill him. Smiling, Elias tells him that he wants him to watch as he reunites the families under one roof.
Simmons calls Fusco to Queens and tells him to get intel on Reese. HR knows that the Feds have a task force out looking for Reese, and they’re helping out Elias because it’s in their own interests. Simmons tells Fusco to call in sick afterward and warns him that he doesn’t want to be working Homicide the next couple of days.
Reese tells Finch that they’ll have to take the direct approach and goes to one of the mobsters, Caparelli, as he leaves a restaurant. When Reese tries to tell him about Elias, Caparelli says that he isn’t interested. As they drive off, their SUV explodes, injuring several nearby pedestrians. Reese sees Scarface drive away, smiling in satisfaction.
A 12-year-old Elias goes to see his foster mother, Gloria, a manicurist, and complains that the kids at school started a fight with him. She points out that he never turned in his term project, which is about his family tree, and Elias insists that he’s not a bastard. Gloria offers to help him fill it out but Elias says that his mother is gone and he doesn’t have any family. He wants to fill in his father’s name and begs Gloria for anything that she knows, but she tells him to let it go and be his own man.
Elias waits with his father and gets a call from Reese. Reese tells him to end it before anyone else gets hurt, but Elias insists that he’s doing what is right. He reminds Reese that he’s a killer and suggests that he stick to innocent men, but Reese says that he can’t do that. Once he hangs up, Finch tells Reese that he’s been monitoring Carter and knows that she’s reaching out to the remaining Dons, offering police protection. She doesn’t know that Elias plans to take them out and has HR backing him, and Reese leaves to protect her.
That night, Carter takes several cars of uniforms to bring in Don Basile, and takes one of them to collect the mobster. Basile is skeptical but Carter says that she doesn’t have a choice. As they take him back to the cars, they discover that they’re all gone. A killer shoots and kills Basile and wounds the cop, but Reese arrives in time to kill the shooter.
A 22-year-old Elias drops off a delivery for Gianni, who is eating dinner with his son Gianni Jr. Once they’re alone, Gianni says that he knows Elias’s mother, Marlene Elias, and asks what he wants. Elias says that he just wants a job and a chance to learn from the best. The mobster tells him that he didn’t know his father and he survived, but assures Elias that there’s a place for him in his operation. As Elias leaves, he says that it’s nice to finally meet him.
Carter gets the officer to the hospital and then meets Reese at a diner. She warns him about the FBI task force as Finch arrives and admits that she doesn’t know who to trust. Finch assures her that they can trust her, and she tells them about the $4 million transfer. Since she can’t access the databases without a warrant, Finch offers to pursue his own leads so they can find the men on Elias’ payroll. That leaves Carter to convince the remaining Dons to take police protection. Reese gives her a bag of weapons in case he’s not there and she reluctantly accepts them before leaving.
The next morning, Carter is checking the weapons when Fusco meets her. She tells him that he’s the only cop he can trust and has him go with her.
Finch has Reese follow one of the payees, who is following a family in the park. Reese realizes that it’s the Simmons family, and that Elias is prepared to coerce his allies as well as his enemies.
The remaining Dons meet at the club and Carter and Fusco arrive. She tells them that they’re going into protective custody because they failed to make a deal, and she’s not going to let innocent civilians get killed. The Dons call for their bodyguard to usher the officers out, but get no answer. Carter warns that their men are abandoning them but Gianni Jr. still refuses to cooperate. She draws her gun on him and admits to Fusco that they don’t have any backup. The Dons go with them and head out to the SUV as Elias’ men charge out of the club. Carter fires on them while Gianni Jr. gets a call. It’s Finch, who directs her to a prepared safehouse.
Elias is playing solitaire and talking to Gianni Sr. about his mother, who died when he was 4. He relates what he can remember of her but admits that many times he just sees the blood. Scarface arrives and tells his boss that Carter took the remaining Dons into protective custody. Elias tells Scarface to call in HR to help track them down.
Finch tells Reese that Carter has gotten the three Dons safety. Reese has tracked down several of the men that Elias paid off and cloned their phones. However, he realizes that they're near the high school where Taylor goes to school. Meanwhile, Scarface, posing as a police officer, comes to collect Taylor, claiming that his mother was in an accident. Finch calls Taylor and tells him to stay inside the school with a teacher. Scarface realizes that something is up and yanks the phone away, while a school security monitor tries to stop him. Elias’ henchman guns him down as Reese arrives and shoots down Scarface’s partner. Scarface himself drives away before Reese can stop him, using Taylor as a shield.
At the safehouse, Fusco wonders how long they can keep the mob bosses safe. They see two men pull up outside and realize that Elias has already tracked them down. Reese calls and starts to tell Carter that he’ll find Taylor and save him, but Elias calls on Taylor’s phone. He tells her that she’s out of backup and has nowhere to turn. When Carter wonders why he has to kill them given how much power he’s shown, Elias explains that Zambrano sells heroin to school children, Grifoni sells guns, and Gianni Jr. imports drugs and young girls. He assures Carter that he’ll run an efficient operation, but Carter doesn’t buy it and hangs up. She then gets back to Reese, who tells her that she won’t have to decide because he’s giving his word that he’ll rescue Taylor. Reese then calls Finch and tells him to find Taylor, and Finch says he’s already on it but they’re going to have to make a deal with the devil.
As Carter watches the men outside, Fusco asks if she’s okay and she admits that Elias has her son. When he wonders if they need backup, Carter points out the men and warns him that they’re with HR. She tells Fusco to make sure the place is sealed and he leaves. Meanwhile, Zambrano points out to Carter that Fusco used to be on the take, and figures that he’s working with HR. Elias comes up to the door and gets on the intercom, asking Carter if she’s ready to pick the right side.
Finch goes to a diner and asks for a few minutes of Simmons’ time. He sits down and explains that he knows all about HR’s involvement with Elias. Finch shows Simmons photos of the men who are watching Simmons’ family and the other HR men, and explains that Elias has abducted Carter’s son. When Simmons proves skeptical, Finch asks if he’s willing to gamble his own family. The officer asks what Finch wants, and Finch tells him to call off his men working for Elias, get him Taylor’s location, and cut off all ties to Elias.
Carter refuses to open the door and tells Elias to let Taylor go. As his men prepare to cut through the door with an acetylene torch, Elias says that he’d rather not hurt Taylor and Carter has to accept that no one is coming to save her. When Carter says nothing, Elias tells his men to start cutting. As he waits, Elias, examines a scar on his hand.
Two of Gianni Sr.’s men lure Elias out into the woods on their boss’ orders and inform him that Gianni wants him dead. Elias tells them that they’re not safe because they outnumber him, and he gets his strength from being alone. He vows to destroy them all and one of the men tries to garrote him. Elias uses him as a shield and lets the other man shoot his partner, then shoots the second man down.
Reese and Finch arrive at the address where Elias is holding Taylor. Finch wishes that he could be more help and offers to shoot a gun and create a distraction. Reese tells him that he can be the getaway driver and that he doesn’t like it when people mess with kids.
Elias gives Carter one more chance to surrender, but she grabs a gun and tells the crime lord that she’s not as alone as he thinks.
Reese shoots a man through the door and barges in. He exchanges shots with Scarface and his two men, kills one, and goes for Gianni and Taylor. The other man goes after Reese and he takes him out, while Scarface make his escape. Reese assures Taylor that his mother sent him, and then tells Gianni that he’s there to rescue him... this time.
Fusco notices that the HR cops are leaving and tells Carter. Zambrano grabs Fusco’s gun and tells Carter to surrender, and admits that he made a deal with Elias to betray the other Dons. Carter refuses to back down, but Zambrano says that Fusco knows which side to choose.
As Elias’ men finish cutting through the door, they hear gunshots inside. They bust in and find Fusco and Carter, waiting for them. The police pull up outside and Fusco said that he called for backup, and that Elias doesn’t own every cop. Realizing that he’s outclassed, Elias tells his men to surrender but warns Carter that change is inevitable. Gianni Jr. demands to know where his father is and vows to kill Elias, and Taylor calls to assure her that he’s safe.
The next day, Reese reunited Taylor and his mother, and Carter thanks him for keeping his promises.
Elias is fingerprinted and photographed.
The Morellis are reunited and they get into the car. They hear a phone ring and finally locate an envelope holding a cell phone and a photo of the dead Marlene Elias. Gianni Sr. answers the phone and Elias tells him goodbye, and wishes he could be there. Their car blows up as Scarface looks on, and Elias hands his cell phone back to the guard and goes into his cell.