A man receives a call that they have the target, and insists that he wants to be there himself to make sure that the target is killed.
A man is killed at a bodega and Carter and Fusco are called in. Fusco dismisses it as an insignificant shooting, but Carter figures it for a professional execution. They go over the security footage and determine that there was a witness. They put out a bolo and Fusco figures that the witness will try and disappeared. The detectives meet with Detective Szymanski with Organized Crime Division, and he explains that the victim was a Mob lieutenant Benny D'Agostino, who disappeared until recently. Benny's boss ordered hits on rival Russian mobsters and Szymanski figures that the hit on Benny was retribution ordered by Ivan Yogorov, the brother of one of the dead men. All they know about Benny's boss is that his name is Elias. They go back over the security footage and confirm that Benny said something to the witness. They figure the owner will tell the Russians and that they'll start looking for the witness to eliminate him.
Finch has received the number of the witness, Charlie Burton, and Reese watches him apartment from across the street. Charlie is a high school history teacher who lives alone. Fusco calls Reese and asks for help finding the witness, and his description matches Charlie's. The Russians pull up at Charlie's building and Reese goes around the alleyway and into the teacher's apartment. Charlie draws a knife on him and Reese tells him that the men from the bodega are there. Charlie has no choice but to go with him and they get out just ahead of the hit squad. They head out the back and Reese takes out the man left on guard after a struggle.
To get out of the neighborhood, Reese figures they have to go through some tenements. Charlie warns him that a Bulgarian drug dealer controls the territory. When Reese tries to call Finch for another route, he discovers that his cell phone was destroyed in the fight. Charlie doesn't believe in cell phones. Meanwhile, Finch discovers that he's lost contact with his partner.
Reese steals a car and tells Charlie that he has to testify to the police, explaining that he knows a detective they can trust. The Russians find them and open fire, wounding Charlie in the shoulder. Reese realizes that they have no choice but to go into the Bulgarian's territory. They enter one of the tenements and sneak into an abandoned apartment. Reese confirms that Charlie isn't badly injured but will need treatment for infection. Charlie tells his rescuer that he saw the killers at the bodega, and one of them showed his face to Benny to make sure he knew had killed him. Benny gave Charlie a message for Elias, a message for a Vinnie that he would finish the job for him. When Reese wonders why Charlie didn't go to the police, the teacher says that he doesn't know which police officers he can trust. He refuses to testify and be forced to abandon him students, but Reese warns that the mobsters won't stop until he's dead. After a moment, Charlie thanks Reese for saving his life and Reese introduces himself as John.
At the precinct house, Carter, Fusco, and Szymanski call in Benny's wife, Patti. She isn't interested in their condolences and Fusco asks why Benny was in Brighton Beach conducting business. Patti refuses to talk at first, and Carter says that she knows what it feels like to lose someone you love. Patti says that it won't do any good and that Elias will kill wipe out the Russians. She isn't interested in the innocents that will be hurt in the crossfire and says that she's never met Elias. When Fusco wonders what Elias wants with Brighton Beach, Patti says that it's just the start of his plans to reunite the Five Families, take out the Russians, and then force the police to answer to him.
Finch goes to an ATM across the street from Charlie's apartment and reroutes the camera, and then limps away as Carter and Fusco arrives. Szymanski brings them up to speed on Charlie's escape, and Carter recognizes Reese from his description. A witness got a photo of the man in charge, Peter Yogorov, Ivan's son. Carter has a cop with a facial scar run down Peter's location. Meanwhile, Finch returns to the library and accesses the ATM footage of the shootout. Once Reese and Charlie escape, Finch sees footage of the scarface cop getting into a SUV outside Charlie's building, He then makes a voice-filtered call to Fusco and tells him to run the license plate on the SUV.
Peter and his brother, Laszlo, arrive at the tenement. Laszlo is eager to go in, but Peter warns that they have a deal with the Bulgarians to stay out of each other's turf. They surround the building and wait for Charlie to come outside. Meanwhile, Charlie starts to slip into shock and asks Reese how he got involved in protecting people. Reese avoids the question and asks Charlie if he always wanted to be a teacher. The teacher explains that a lot of his students are affiliated with the Russian Mob and he's tried to give them a different life. Reese tells Charlie to stay put while he goes to get some antibiotics for Charlie's wound.
Finch meets with Fusco on the street, and the detective confirms that the van belongs to a shell company and it's a dead-end. The programmer tells him that Elias is also after Charlie for the message that Benny passed on. Finch tells him to report the SUV from outside Charlie's apartment as stolen and email the report number to an address. As Finch leaves, Fusco asks him if he's heard from Reese and Finch admits that he hasn't.
Reese confronts two of the drug dealers in the tenement and asks for their drugs. When they come after him, Reese easily subdues them and takes what he needs.
Carter and Fusco go over the case with Szymanski, who figures that Ivan may have been at the bodega to avenge his brother's death in person. Elias is always one step ahead of the Russian Mob and the police, and Szymanski wonders why the mobster is interested in Brighton Beach. Carter shows him the file on Carl Elias and they figure that he's come back to clean up the neighborhood that his birth father ran before he died, and claim his birthright.
Reese treats Charlie with cocaine and glue and the teacher thanks him for everything that he's done. Once he's done, Reese offers Charlie a gun to use in case of emergency. The teacher reluctantly takes it and wonders if they can get out, and Reese says that their odds are better now that they have Charlie patched up.
Peter and Laszlo meet with the Bulgarian dealer and offer to take out Reese and Charlie and take care of the Bulgarian's problem. He agrees and they go inside. Meanwhile, Reese has Charlie put on a coat and then tries to find a live phone wire in the walls. As Reese works, Charlie wonders why he's taken such a risky career choice and Reese points out that he sounds like Finch. He then calls Finch and tells him where he is, and Finch brings up the city blueprints and finds two service entrances. Reese tells Finch to have Fusco meet them at the ferry the next morning at 7 a.m.
Reese takes Charlie to the service stairs but they're force to drop back when the mobsters show up on the floor. As the bad guys close in, Reese tries to find an empty apartment to hide in. One of Charlie's students, Will, lives in the tenement and sees them. He wonders what Charlie is doing there and the teacher claims that they got lost. Will realizes that they're on the run and invites them into his apartment to hide while his father is out.
Finch receives the stolen car report from Fusco, calls Vehicle Recovery Services, and poses as Fusco to get them to turn on the SUV's GPS locator and microphone.
Will explains that he and his father are planning to move as soon as his dad gets a job. Charlie tells him to do what he can to get to school.
Finch tracks the GPS locator on the SUV and listens in the scarface cop gets word that the Russians are in the tenement. As he leaves, Finch considers his surveillance photos of the cop and wonders if the man is Carl Elias.
Peter knocks at Will's door and the boy answers it. He assures the mobster that he's home alone but refuse to let Peter in, insisting that he won't back down. Impressed, Peter leaves and Charlie thanks his student for his help. The painkillers start to wear off and Reese wonders if he can get to the service stairs. Will suggests that they go down the old stairs and Reese takes Charlie out. When Peter and Laszlo come down the hallway, they duck in to the first apartment they hid in. The brothers briefly check the room and Peter goes on to the next room. Reese grabs Laszlo and captures him at gunpoint.
Carter and Szymanski go to see Ivan and demand to know where they can find Peter. The mobster insists that Peter was there all day working for him, and has gone to get wine for an event. Szymanski wonders if he's willing to let his sons get killed in the mob war, but Ivan says that Elias is the one who is intruding into his territory and killing his people.
As they move out, Reese uses Laszlo's cell phone to call Finch and have him notify Carter that the bodega killers are in the tenement. They go down the old stairs and out into the street.
Finch listens in on the SUV's microphone and hears Scarface say that they've got a text that Reese and Charlie are at the ferry.
Carter and Szymanski go to the tenement and arrest Peter for the bodega murder. Meanwhile, Fusco is on the pier waiting for the ferry when Finch calls him and accuses him of selling out Reese to Elias. Fusco insists that he had nothing to do with it, and Scarface knocks him out from behind.
As they cross on the pier, Reese asks Charlie to testify. The teacher says that he'll do it and get the Yogorovs off the street.
Carter goes to see Peter in the interrogation room and tells him that they have an ironclad case against him.
Charlie thanks Reese for making sure he lived to see another day.
Carter tells Peter that she's figured that he and his family went to the bodega to kill Elias. However, they had no idea what he looked like so settled for murdering Benny. Peter admits that they had a call that Elias was meeting Benny at the bodega, but when they showed up, only Benny was there. They talked to the owner later, who confirmed that there was another guy there.
Laszlo, tied up to a pipe, asks Reese how he can work for a scumbag. Reese asks him what he means and Laszlo realize that he doesn't know who Charlie really is.
Peter tells Carter that they wouldn't have bothered going to such trouble just for a witness.
Laszlo warns Reese that he has no idea what he's involved in. Charlie draws a gun on Reese and tells him to turn over his gun. He complies and Charlie/Elias explains that he learned from his enemy's children what their weaknesses were. Elias tells Laszlo that their children hate them almost as much as he does, and has Reese ties himself to the railing. He figures that it's time to move onto the next step and prepares to shoot Laszlo. Laszlo tells him to kill him and Elias says that Benny said, "Veni, Vidi, Vici,"not "Vinnie." The Latin phrase means, "I came, I saw, I won," meaning that Elias had already won and that the Yogorov empire is already crumbling. He then shoots Laszlo in the leg and tells him to inform his father that if he gets out of tonight that night, Elias let him live. He then turns to Reese and says that he considered killing him, but would rather have him in his organization. Reese says nothing and Elias tells him that they're better off if they don't meet again. When Reese asks what happens if they do meet, Elias warns that it'll go poorly for him.
Elias escapes with Scarface.
Finch comes to see Fusco on the pier and apologizes for misjudging him. They greet Reese as he gets off the ferry and tells Fusco that his prisoner is on the boat. Finch goes with Reese and points out that the Machine was right, but they didn't know that the intended victim was also a killer. Reese blames himself for saving Elias, but Finch says that they have limited information and they knew that they'd eventually make a mistake. He says that they need to move onto the next POI, but Reese asks how many numbers will come up because they lost Elias.
Later, Scarface walks into Ivan's office and kills him. He and his men then meet Elias and tell him that it's done, but he says that it's just beginning.