The Machine monitors the team discovering that Dominic plans to take down Elias... and Martine tracking down Sam at the department store.
Sam's manager comes over to complain about her work, just as Martine opens fire. Sam shoves the manager down, pulls out a gun, and returns fire. She shoots out the cameras when she realizes that Martine is using them to track her, and heads for the door while returning fire. When she gets outside, Root is waiting with a motorcycle and they drive away. Once they reach a camera dead-zone, Root pulls into a moving van and covers the motorcycle over. She tells Sam that her cover has been blown and they hide in the back as the moving men finish up and close the door.
As the truck moves off, Root tells Finch that she rescued Sam. He points out that the Machine didn't register Sam as a Number because Samaritan's operatives have learned to operate in the shadows just as they have. Finch tells them to use the shadow map to avoid all cameras, and sends assistance to their location. Sam wonders what she'll do if they get a new Number, and Finch assures her that Reese can handle it.
Reese is following Elias and Scarface walking on the boardwalk. Finch checks in with his teammate and reminds him that Dominic has all known information on Elias. He also reports that Sam has been compromised but tells Reese to stay with Elias. They both agree that it's better to have Elias controlling New York's underworld than Dominic. Meanwhile, Elias meets with one of his people, Bruce. Finch identifies him as Bruce Moran, an investment advisor and CPA... and Elias's money man. Bruce tells Elias that the Feds are sniffing around but he has nothing to worry about. Reese spots Link with the Brotherhood tracking Elias and let's Finch know.
Fusco pulls the moving truck over in a dead zone and get Root and Sam out.
Reese approaches Elias and Scarface in a parking garge, and explains that Dominic stole the NYPD cache of information on Elias. Elias believes that he's in danger but says that he can handle the newcomer, and Reese points out that the old dons that Elias took out thought the same thing. Despite that, Elias says that he doesn't need help and walks away to his hideout in the basement of the garage. The man at the door, Ricky, prepares to shoot Elias in the back but Reese takes him down and closes the door. More men move in and Elias assures Reese that he has another way out.
Once they reach the street, Reese insists that they have to get out of the city. Elias refuses to run and let Dominic win, and tells Reese that he doesn't want his advice. They drive to an Italian restaurant owned by one of Elias's people, Gino. Gino offers his assistance, but both Elias and Reese realize that Gino and his men are jumpy. Everyone goes for their guns and they end up in a standoff, and Gino admits that Dominic got to him. Gino doesn't know if Dominic has gotten to Bruce, and says that Dominic's people will be there in less than a minute. As Elias leaves, he promises Gino that he'll be back for im.
Martine finds the moving truck and checks in with Greer. He has identified Root, and Martine reports that Samaritan couldn't see Sam. Greer wonders how they're doing it, and Martine says that the truck was pulled over in a dead zone by a detective and she's looking into it.
Sam and Root head down the street and Sam says that the Machine needs to give her a new identity. Root says that the Machine won't do it and figures that Sam should be scared. When Sam says that she isn't scared, Root says that she should be and that people who care for her are scared.
Dominic and Link arrive at Gino's and the owner describes what Elias said. Link brings out the photos he took of Bruce, and Gino says that Bruce is Elias' business advisor. Dominic assures Gino that he'll have more territory than ever, but Gino is concerned that Elias is still at large. The Brotherhood leader says that Elias won't be a problem for long, and figures that Bruce is much more than just a money man. Dominic figures that Bruce was the one who handled all of Elias' business when he was in prison and on the road.
Elias goes to a building that he bought and renovated, and tells Reese that Bruce is there and he needs to pick up something important. The Brotherhood pull up at the front and back, and Elias leads Reese and Scarface to the penthouse elevator. Reese points out that they'll be cornered but elias tells him to have some faith and they go up as the Brotherhood enter the lobby.
As they go up, Finch checks in with Reese. They can't call for police backup because then Elias will end up in prison, an easy target for Dominic's killers. As Finch notifies Fusco, Elias hits the emergency stop on the elevator and gets out on an unrenovated floor.
Finch calls Fusco just as Martine comes in, claiming to be a DEA agent. She wants to know why Fusco stopped the moving truck for a drug search when he works homicide. Finch accesses the hidden camera on Fusco's desk and realizes that Martine is working for Samaritan. Fusco claims that he's working a joint operation with Narcotics and DEA knows about it. As he starts to call the DEA, Martine tells him that it isn't necessary and leaves. Fusco gets back to Finch, who warns him that Martine isn't DEA but can't fully explain. Realizing that he can't compromise Fusco and put his life in danger, Finch tells Fusco that they don't need his help after all.
Elias and the others get to Bruce's office. Bruce isn't there, and Elias opens a secret door that he kept from the previous owners. As he goes to his vault, the Brotherhood break in and open fire, and Reese gets Elias out while Scarface provides cover fire. One of the Brotherhood men nails him in the shoulder, and Scarface tells Elias to go. Reese tries to go back for him but there's too much fire and he's forced to take Elias downstairs.
Samaritan operatives drive past Root and Sam, who hastily look away. Finch checks in with them and warns that Martine talked to Fusco, and that he's going to assist Reese. Sam realizes that they're working a Number and demands answers, and Finch finally admits that Elias is their new Number. She demands to know where Reese is, but Finch cuts her off. Sam insists that she doesn't need protection and begs Root to tell her where Reese is. She refuses to go until she gets an answer, and starts to step out in front of the cameras. Root drags her back and says that they'll help Reese, but then Sam goes underground.
Elias and Reese descend through the building and Elias leads Reese into another unrenovated apartment. Reese warns that they don’t have much time, but Elias is more concerned about Scarface's fate. Dominic calls and says that he has Scarface, and says that he wants to do to Elias what Elias did to the dons. The Brotherhood leader offers to let Reese and Scarface go if Elias surrenders himself. If Elias refuses then all three men die.
Reese confirms that it's all clear and says that it's time to go. He realizes that Elias plans to give himself up, and warns that Dominic is likely to kill them all despite his promises. Elias refuses to abandon Scarface and Reese promises to come back for him once he gets Elias to vaultty. He gives Elias a gun and Elias reluctantly takes it.
As Dominic's men break into the vault, Dominic tells Link that they're after more than just money. He figures that the vault has the information Elias has used to build his organization and run the city. He asks Scarface for the combination, and Scarface claims that he doesn't know it. Dominic doesn't believe him and invites him to join with him... or die. Scarface just chuckles and Dominic beats him.
Elias and Reese make their way through the building and Elias admits that the previous owners never put any money into it. The Brotherhood gangers search floor by floor, forcing them to take cover. Reese checks in and Finch tells him that Fusco is unavailable and he's on the street. Finch has hacked the penthouse wifi system as a form of radar, and can only find one possible exit.
Dominic tells Link to torture Scarface until he give sup the combination, and then leaves with his men. Link sits down and says that he figures that Scarface doesn't know the combination. He advises Scarface to take Dominic's offer, but Dominic says that he already has a boss that he'd lay his life down for. He tells Link to think about his own future or he could end up the same way as he has.
As they head for the exit, Elias explains that he and Scarface met in a group home. Scarface--Anthony--killed his father for beating on his mother, and he and Elias hit it right off. Elias wonders how much further Reese is willing to go, and Reese says that he just wants to get to the exit.
Sam and Root avoid the cameras and arrive at the building. They find an open door and go inside, and Reese realizes that they're in a gymnasium. Root injects Sam with a sedative, saying that she didn't have a choice. Sam says that she's going to end her and passes out.
Reese gets Elias to the exit, but Elias aims the gun at Reese and says that he's not letting him go back in. He knows that Reese would die trying and goes back in to negotiate for Scarface's life. He goes in and locks the door behind him, and Finch calls Elias and begs him not to give his life up. He warns that there's more hanging in the balance than Scarface's life, and he's kept the violent criminal element in check. Elias tells his friend that the best he can hope for is to protect those closest to him. Dominic and his men find Elias, who tells Finch goodbye.
Reese gets back into the building and Finch gives him a possible location where he's detected people moving.
Dominic ties Elias up and admits that he admires him. However, he wants the code to the vault before he lets Anthony goes. Elias wonders if Scarface is still alive, and Dominic calls Link to put Anthony on. Anthony confirms that he's alive and a ganger beats him. Elias refuses to give Dominic the code unless they release Anthony, and Anthony says that's not going to happen. He tells Elias that he just wants it to be done, and Elias agrees. Elias says that his friend has gone far enough and then gives Dominic the code.
Finch scans the vault and warns Reese that there's something strange about it.
Elias gives Dominic credit for infiltrating his organization and identifying his weaknesses.
Finch stares at the vault schematic ion shock.
As Dominic draws his gun, Elias says that he knows Dominic's weakness: pride. Realizing that something is wrong, Dominic calls Link and tells him not to enter the code. It's too late, and Link runs out of the room just as the vault explodes, blowing out the entire penthouse. Dominic tells Elias that he's still won, but Elias points out that he's not smiling. Before he can pull the trigger, Reese arrives and opens fire. Dominic walks out while Reese takes down his men and tells Elias to go.
The next day, Finch and Reese wait for Sam to wake up. Finch says that their survival now depends on Sam's seclusion, and says that they must proceed with extreme caution.
Martine returns to Decima and Greer tells her that the Machine is blocking all relevant data about Finch and his associates. To bypass that, they're going to rely on human intelligence. Greer says that he's expanding her capabilities and provides her with a team.
An injured Link reports to Dominic, who says that he's not worried about Elias. Link points out that they lost a lot of good men, but Dominic figures that Elias has someone protecting him. If they find out who is bankrolling Reese and Sam, then they'll have a handle on Elias.
Bruce meets Elias on the boardwalk and offers his condolence. Elias shows him a photo he saved of the three of them in the group home, and Bruce assures him that the principal assets are offshore and untouchable. The crime lord says that they'll arrange a new office for Bruce, and they won't meet again because he doesn't want to lose another friend. Bruce says that he has a list of everyone that switched sides, and Elias says that they're going to start with Gino.
Once Bruce leaves, Elias calls Finch and thanks him and Reese for their help. He explains that the building was a failsafe, and Finch has confirmed that the building used to be a group home. Elias admits that he never liked the place, and Reese apologizes for not saving Anthony. The crime lord says that he's going to make sure that Anthony's sacrifice wasn't in vain, and tells Reese and Finch to stay out of his way when he goes after Dominic.. With that, Elias hangs up and walks away... alone.