On the phone, Elias wonders what kind of man he'd be if Gianni Moretti hadn't murdered his mother, Marlene.
As Carter drops her son Taylor off at his high-end school, he admits that a rich student is taunting him because he's there on a scholarship. Carter volunteers to take care of it but Taylor says that he'll handle it, and that he'll take the subway home that night because he knows that she's busy. Once he goes inside, Carter gets a call from Detective Sherri Lablanca in SID, who informs her that Elias has removed the $4 million from his bank accounts that he made on the recent investment scam.
Finch informs Reese that the Machine has given them five numbers: the five dons of the New York Mafia. One of them is Gianni Moretti Jr., who took over when his father went to prison. They figure that Elias is making his move after kidnapping Gianni Sr.
The Dons meet at the Covenant Club and Finch hacks the emergency fire system speakers to listen in. Gianni Jr. is disgusted that the other four men are going to look the other way on Elias' kidnapping of his father since Elias is making them money. As Finch and Reese listen in, Finch suggests that Reese call and apologize to Carter and get her involved. However, Carter is with Lablanca and ignores the call. The SID detective has confirmed that Elias shipped out the $4 million in cash and wire transfers to a thousand payees, and it will take months to get all of the search warrants necessary. Unaware that Fusco is listening in, Carter figures that Elias is using the money for bribes and payoffs.
Elias is keeping Gianni Sr. at a winery and brings him some food, but is careful not to give him a knife. He tells Gianni that he and the others have gone soft and that he's going to remedy that. When Gianni asks why he didn't just kill him, Elias tells him that he wants him to watch as he takes complete control of the New York underworld.
Simmons with HR meets with Fusco and tells him to track down Reese, When Fusco wonders why, Simmons explains that HR knows about the FBI task force and that HR is helping Elias. He then tells Fusco to call in sick for a few days because he won't want to be working Homicide with what's coming.
Reese tells Finch that he's going to take the direct approach and goes to one of the Dons, Caparelli, as he leaves a restaurant. However, Caparelli isn't interested in what Reese has to say and figures his men can protect him. As he drives away, his vehicle blows up, injuring several pedestrians, and Scarface drives away.
A 12-year-old Elias gets into a fight at school and goes to the shop where his foster mother, Gloria, works as a manicurist. He finally admits that they called him a bastard and insists that he isn't, and shows Gloria the blank family tree he was supposed to fill in for his school project. She offers to help him fill out but Elias insists that he doesn't have a real family. He asks Gloria what his father's name, desperate to find out anything about him, and Gloria tells him that he has to be his own man and let go of the past.
Reese calls Elias on the burner cell phone and tells him to stop before anyone else gets hurt. Elias refuses, insisting that he's doing what he has to, and points out that both of them are killers. When he tells Reese to stick to protecting innocent men, Reese says that he can't. Once Elias hangs up, Finch tells Reese that he's been keeping an eye on Carter and she's offering police protection to the four surviving Dons. Since she's unaware that Elias has bought off HR, they figure she's in danger from her own men and Reese leaves to protect her.
That night, Carter takes two cars of officers to pick up Don Basile. She and one her officer escort Basile from his office to his car only to discover that the other cops have left. One of Elias' hired guns opens fire, killing Basile and wounding the officer. As Carter tries to shoot back, Reese arrives and dispose of the killer.
A 22-year-old Elias is now working for his father, Gianni. He makes a delivery at the restaurant where Gianni is eating with Gianni, Jr. Gianni recognizes Elias and sends his other son off, and then says that he knows that Elias is his son and Marlene was his mother. He asks what he wants and Elias explains that he just wants a chance to learn from the best. Gianni points out that he survived even though he didn't know his father, but offers Elias a place in his organization. As Elias leaves, he tells his birth father that it's nice to finally meet him.
After getting the wounded officer to the hospital, Cart meets Finch and Reese at a diner. She warns them about the FBI task force and Elias' $4 million transfer, and asks Finch to look into it. He assures her that he'll find the men on Elias' payroll, while Carter says she's going to warn the remaining three Dons. Reese gives her a bag of weapons in case her plan doesn't work and she takes them with her.
The next morning, Carter calls Fusco and has him meet her. She admits that as her partner, he's the only cop she can trust and he agrees to go with her to take the Dons into police protection.
Once he starts tracking down the men that Elias paid, Finch has Reese follow them. One of them follows Simmons' family and Reese realizes that Elias plans to threaten HR's families if and when he has to.
Carter and Fusco finds the three remaining Dons at the Covenant Club, and she insists that they come with her so Elias doesn't endanger anyone else trying to kill them. She reminds them that they ignored Elias and are paying the price, and she's going to have to clean up after them. They call for their bodyguard but discover that he's already fled, and Carter draws her gun and orders them to come with her. Fusco backs her and the Dons reluctantly go out to Carter's van. As they drive away, Finch calls Carter on Gianni Jr.'s phone and gives her directions to one of his safehouses.
As Elias plays solitaire and tells Gianni what little he can remember of his mother before Gianni killed her, Scarface arrives to report that Carter has the remaining Dons in protective custody, and Elias tells him to call in HR.
Finch updates Reese on Carter's whereabouts. Reese realizes that one of the men he's been following is near Taylor's school. By the time he gets there, Scarface has already gotten the boy out by posing as police officer taking him to Carter. Finch calls Taylor and tries to warn him, but Scarface realizes what's going on and takes away the phone. When a security monitor tries to intervene, Scarface shoots him and heads for the car with his partner. Reese arrives and gun down the other man, but Scarface gets Taylor into the car and uses him a shield to get away.
At the safehouse, Fusco and Carter see two plainclothes officers pull up outside, but Carter realizes that they're with HR. Reese calls and starts to tell Carter what happened, but Elias calls her via Taylor's phone and tells her that he has her son. Carter refuses to turn over the Dons, even after Elias tells them that they sell drugs and guns to children, and sell children into prostitution. She doesn't believe that he's any better but Elias assures her that he'll run an efficient operation. Carter hangs up on him and gets back to Reese, who promises her that he'll bring Taylor back to her. He then calls Finch, who says that he's going to have to cut a deal with the devil to find out where Elias is keeping Taylor.
As Carter and Fusco wait and watch the men outside, he asks if she's okay and Carter tell him that Elias has Taylor. Fusco figures that it's time to call in backup, but Carter warns him that the men outside are with HR. He goes around the apartment to check the doors while one of the Dons, Zambrano, tells her that Fusco used to be on the take and probably still is. Elias pulls up and calls Carter on the intercom, asking her if she's ready to choose the right side.
Finch tracks Simmons down to a diner and sits down with him. When the officer wonders what he wants, Finch explains that he knows about HR and how they're working with Elias, and then shows Simmons photos of the street thug following his family. He explains that Elias has abducted Carter's son and asks if Simmons is willing to gamble his own family on someone willing to abduct an officer's child. When Simmons wonders what Finch wants, Finch tells him to have HR stop working with Elias and find out where Taylor is being held.
When Carter refuses to let Elias in, he orders his men to use an acetylene torch to cut through the metal door and tells Carter that he'd rather not have to hurt Taylor. However, he warns her that she's all alone and no one is coming to save her. While he watches his men go to work, Elias looks at a thin scar on the palm of his hand.
Two of Gianni's soldiers take Elias out to the forest, saying his father has a job for him. However, once they get there, they tell Elias that they've been ordered to kill him. Elias dismisses them as weak, saying that they out number him but they're not strong. He tells them that he gets his strength from being alone and that he'll destroy them all. One of the soldiers tries to garrote him with piano wire but Elias catches it on his hand and swings the man around so that his partner shoots him. Elias then grabs the first soldier's gun and shoots the other man dead.
Once HR gets Taylor's address, Reese and Finch drive there. Finch wishes that he could be more help and offers to take up a gun, but Reese tells him to stay in the car and be ready to drive away. As he goes in, Reese says that he doesn't like people who mess with kids.
When Elias gives her one more chance to surrender, Carter aims her gun and tells Elias that she's not as alone as he thinks.
Reese shoots the man at the door by aiming through the door, and then kicks his way in. He fires at Scarface and the other two men, taking out one. Reese then gets to the back and finds Gianni and Taylor, and the other man attacks him. Reese finally takes him out but can only watch as Scarface runs out the back door. Once he unties Taylor, Reese tells the boy that his mother sent him. He then turns to Gianni who wonders if he's there to rescue him or kill him. Reese says that he's going to rescue him... this time.
The HR cops outside the safehouse leave and Fusco tells Carter. However, Zambrano grabs Fusco's gun and aims it at Carter. He tells her to let Elias in and Gianni Jr. realizes that Zambrano has been working with Elias all along. Carter refuses to back down and Zambrano warns her that Fusco used to be crooked.. He figures that Fusco is still crooked and that he'll make the right decision to throw in with Elias.
Elias and his men hear gunshots inside as the finish cutting through the door. When they come in, they find Fusco and Carter waiting for them together, guns aimed. The police pull up outside and Fusco tells Carter that she has to trust someone, and that Elias doesn't own every cop. Elias gracefully surrenders and orders his men to do likewise, and warns Carter that change is inevitable. Gianni Jr. demands to know where his father is, and Taylor calls to tell his mother that he's safe and that Reese rescued him and Gianni.
The next day, Reese brings Taylor to Carter. She thanks him for keeping his promise to her.
Elias is booked at the station.
Gianni and his son are reunited and get into their car. They hear a phone ring and finally find an envelope containing a cell phone and a photo of Elias' dead mother, the woman that Gianni killed. When Gianni answers the phone, Elias says goodbye and wishes that he could be there. As Gianni wonders what he means, his car explodes as Scarface looks on. In prison, Elias hands the cell phone to a guard and goes quietly into his cell, satisfied.