The Machine monitors a conversation about the death of an engineer, Justin Lee, at Rylatech. The people involved discuss Monica Jacobs, who is looking into Lee's "accidental" death, and they resolve to stop her.
Elias and Finch are playing chess and Finch asks Elias about his strategy. He explains that he's trying to learn how to win at a disadvantage, and Finch realizes that the deaths of the DA and Szymanski benefited Elias' enemy, Yogorov. Finch also knows that a number of Elias' associates on the inside have been transferred. Elias asks who Finch is playing against and then says that he doesn't know who but he'd like to identify them. Finch warns his opponent that it looks like Elias' loss is a foregone conclusion, but the crime lord tells him that he still has a few moves left as he returns to his cell. Once Finch is alone, the pay phone on the wall rings.
Reese is in the country watching the Coles, who are related to a prior Number. Finch calls to tell Reese that they have a new Number, Monica Jacobs. Monica is a senior VP at Rylatech, a top networking company. As he talks to Reese, Finch passes through Rylatech security after getting a valid ID... as an IT technician at the company. Monica is a rising star at the company and Finch figures that the threat to her could come from anywhere. She walks by Finch, discussing Lee's death with her assistant, and Finch clones her phone. Monica notices Finch's processor and they talk the technology briefly, and she's impressed with his expertise.
Rylatech's owner, Martin Baxter, attends a meeting with Monica and the company's Head of Product Development, Ross Haskell, to sell a prospective buyer on their product. When the TOVO executive wants to know why they should bother, Monica explains that they've been supplying state-of-the-art components to numerous companies, including the Department of Defense. She also points out that their rival, Censatek, is known to offer kickbacks to networking executives. Afterward, Martin wonders how Monica knew about the kickbacks, and she assures him that she has spies everywhere. Martin admits that they can't get along without her.
At the precinct house, Carter meets with Tierney, who is running point on the murders of the DA and Szymanski. Tierney explains that Quinn, the only witness, was wounded and couldn't identify the masked shooter. She then takes a call from Finch, who offers his condolences on Szymanski's death. As they talk, Cal comes in and Carter refuses to talk to him as long as Cal won't reveal the name of the CI who claimed Szymanski was dirty. As she walks away, she runs into Fusco. Carter explains about how Szymanski turned up dead once she cleared his name. She figures that Cal is involved and Fusco says he'll find out what he can.
That night, Finch calls Reese, who is still watching Cole. Finch has tapped into the RFID chips of every employee in the building. Reese soon realizes that Finch admires Monica, who claims that he simply recognizes her superior qualities. Monica leaves her office and goes to the R&D department. Finch follows her and watches as she takes out a laptop from the computer storage room. Monica plugs in a flash drive and downloads some files, and Finch hides as a security guard enters the floor. Once the guard has moved in, Monica slips way and Finch wonders why a woman in her position would risk her position.
As Finch talks to Reese, Sam Shaw comes up behind Reese and captures him at gunpoint. Reese signs off and then tells Sam that he thought he'd find her there. He explains that he's watching Darlene and Evan Cole, the parents of Sam's dead partner, Michael. The government framed Michael as a domestic terrorist, and Reese figured that Sam would visit Michael's parents to tell them the truth. He figures that Sam knows that Control will kill Cole's parents to cover their tracks and she's watching over them. Sam tells Reese to pick a different spot and starts to walk away, and Reese says that just because they walk in the dark doesn't mean they have to walk alone.
The next day, Finch is performing IT work and spots Monica leaving her office. He goes in and starts to access the flash drive, but her assistant Jerome Eckert comes in and Finch claims he's doing a security update. When Jerome demands to know what's going on, Finch bluffs his way through, claims he's finished with his work, and walks out.
Fusco confronts Cal in the restroom and demands to know why he's refusing to say where he got the tip on the money planted on Szymanski. The money never made it to evidence, meaning that either Elias or some dirty cops got hold of it. Fusco figures that Szymanski was set up and that Cal knows about it because he's keeping silent. Cal tells Fusco that he knows all about his past history as a dirty cop, and Fusco tells him to stay from Carter. Tierney comes in before Fusco can say anything further, and the detective walks out.
Monica is picking up a printout on Lee when Jerome comes over and offers to help. She tells him that she has a last-minute meeting that she didn't put on the calendar and walks out. Finch follows her to the park and watches as Ross meets with her. She tells Ross that when she sent flowers to Lee's parents, she discovered that no one by that name lived there. All of Lee's history was fake and Monica figures that Lee was a plant working for a competitor. She gives Ross the flash drive that she copied from Lee's computer and found several encrypted emails. Ross confirms that Monica hasn't told anyone else and promises that he'll look into it. As Reese arrives, he "accidentally" bumps into Ross and steals the flash drive, and then sits down with Finch and hands the drive off.
Cal meets with Quinn and assures him that he hasn't told anyone that Quinn was his tip on the Szymanski money. However, Cal has been wondering where the tip came from. When Quinn says that it doesn't matter, Cal points out that a dead cop's reputation is on the line. The mayor's man says that the information was given to him in confidence, but finally admits that once of Elias' men passed on the info. Quinn wanted his godson Cal to get the credit, and suggests that the person asking is jealous. Cal thanks his godfather for the information, hugs him briefly, and walks off. Once he's out of sight, Simmons comes over and asks if Cal is going to be a problem. Quinn hopes that he won't be.
After asking Carter to look into Lee's car accident, Finch returns to Rylatech. He discovers that someone is syncing with Monica's phone and uploading phony telephone calls. Monica comes in and finds security men going through her desk. Martin and Ross are there and inform her that Security found confidential designs on her computer, attached to emails she was going to send to their competitors. Jerome speaks up, saying that Monica has been acting oddly and making off-the-book appointments. Martin orders Security to see her out and warns that they have civil and criminal charges pending. Finch and Reese figure that someone is trying to silence her and won't stop until she's dead.
The next morning, Reese continues following Monica back to Rylatech. Meanwhile, Finch goes over the information on the flash drive and confirms that Lee was a spy working under deep cover. Meanwhile, Monica follows Jerome as he leaves Rylatech, and Reese follows both of them.
Cal goes to see Elias in prison and asks him if Szymanski was on his payroll, unaware that Fusco is listening in on his cloned cell phone. Elias tells Cal to ask better questions and then asks him who benefits from Szymanski's murder. He suggests that Cal knows the truth and doesn't realize it, and tells him that his people tried to pay off Szymanski but he refused the bribe. Elias tells Cal that he was played by HR and then advises him to choose his next move wisely as he leaves.
Carter calls Finch and tells him that Lee's car accident showed no sign of collision or breakdown. The body is gone from the morgue.
Simmons meets with Quinn and warns him that one of their people saw Cal with Elias. Quinn says that it's a shame and Simmons suggests promoting Cal out of New York. However, Quinn tells Simmons to dispose of him instead and walks away.
Jerome is on the street, making a call to his Chinese employers assuring them that Monica is no longer a problem. Monica approaches him and demands to know why he implicated her. When he shoves her away, Reese runs over and slams Jerome into a car, and then demands to know who he's working for. Jerome says that there are too many of them just as a sniper opens fire. Reese gets Monica into a nearby car while the sniper kills Jerome, and then starts hotwiring the ignition. Finch calls to tell Reese that Lee's emails were to his father, a high-ranking Communist official. Lee was spying for his country and they have just picked a fight with China.
As Reese drives off and Finch tells him to head for the new accommodations, Sam enters the library. She explains that she traced the phone number that Finch gave her and he says that her offer to her still stands. Sam shows him a newspaper article about how a CIA leak cleared her dead partner's name, showing he died on a covert operation to stop a domestic terrorism plot. She points out that Cole didn't work for the CIA, so she figures that Finch hacked into the CIA records and created the fake record for Cole. As they talk, Sam sees a photo of Root on the board and asks what Finch knows about her. Finch admits that it's complicated and Sam takes his list of Root's aliases, pets Bear, and walks out.
Reese takes Monica to the safe house and explains that Lee was working for China. She doesn't know why Lee was spying on her and Reese figures that he may have been tampering with her work. Jerome was attached to her to keep an eye on her. Finch and Bear arrive and Monica realizes that Finch isn't an IT guy. They figure that Lee was working with someone on the inside and Monica figures that it's Ross. She wants to go to the police but Finch says that they need to get to the evidence first.
Finch accesses the Rylatech mainframe but is unable to hack the systems. Monica takes over and complains about how the last ten years of her life have been wasted. Once she's in, Finch takes over and Monica that the people at Rylatech are her family and now they think she betrayed them. Finch searches for the hidden network the spies are using, but the hacker at the other end hacks the laptop and sabotages the firmware, shorting out the computer. Monica suggests that they access server directly, but to do so they have to go inside Rylatech. When Reese points out that everyone at Rylatech knows her, Finch asks for her RFID card even though it has been deactivated.
That night, the security guards pick up Monica's card inside of the building. They move off to her indicated location and find Bear, the ID tag on his leach. Finch, parked outside, gives Bear the order to attack and the dog chases the men into a room. Meanwhile, Reese and Monica go to the server room and access the catalog server. Once they install the transmitter, Finch accesses the system and finds encrypted traffic. There is some anomalous data, but Finch ignores it for the moment and locates the end users. The information is coming in from all of Rylatech's clients, and Monica realizes that someone has compromised the company's routers and servers. Finch discovers that their activities have been detected and tells Reese and Monica to get out.
Security guards move in and Reese returns fire and then jumps one of the security guards. He uses the man as a shield when the second guard opens fire, and then kills the second guard. Finch confirms that the guards are coordinating activities through Ross's office. However, when they arrive there, they discover that Ross is dead from a single shot to the head. Martin comes in with a gun and orders Reese to drop his weapon.
Martin insists that he's protecting his company. Rylatech went bankrupt during the dotcom burst, and Martin saved the company by selling out to China. He explains that by controlling information, they can control the future. Martin knew that Monica and Ross couldn't be trusted with the truth because they believed that the company stood for something. Now he plans to frame Monica for Ross' murder after disposing of her. Finch tells Reese that he's notified the authorities and sent the evidence to the FBI, and Reese warns Martin that his plan won't work.
As they talk, Greer calls Martin and tells him that the time has come and his family will be provided for. Martin says that he understands and hangs up, and then puts the gun to his head and shoots himself. Reese and Monica confirm that everyone has left. Meanwhile, a payphone near Finch rings.
At the precinct house, Fusco calls Carter into a private room and plays the conversation between Cal and Elias. Cal is innocent, and Carter wants to turn the recording over to IAB. Fusco points out that the tap wasn't legal, and tells her that the only way they can find out who gave Cal the tip is for Carter to ask him.
Cal meets with one of his CIs, Donnie, and then prepares to break up a drug deal. Once Donnie leaves, Carter calls Cal and offers to buy him a drink and have a talk. He agrees and hangs up, and the dealers run off into a nearby building. Cal goes in after them and finds Donnie waiting. Donnie tells the dealers to let him get clear. Once he does, the dealers open fire on Cal, who calls for backup.
Finch calls Carter and tells her that Cal's Number has come up. Fusco arrives and tells Carter that they've got a backup request from Cal's location. When she and Fusco arrive there, they discover that Cal is dead. As Carter stares in shock, Fusco gently ushers her away.
The next morning, the newspapers are reporting on the murder-suicide of Martin and Ross. Rylatech's stock has plummeted and the FBI is investigating the rumors of spies and replacing all Rylatech servers. Finch and Reese met with Monica, who tells them that she's received an offer of employment from a company named IFT. Finch wishes her well and Monica leaves. Reese figures that Finch is going to miss her, and Finch says that he would if he had time. However, there's a matter they need to discuss. Finch tells Reese that he recognized some of the encrypted code as identical to the virus Kara uploaded. He's cracked the virus' code and learned that most of the stolen data went to the organization that called Martin. The only name Finch could come up with is Decima Technologies, and he believes that the virus was created to go after a single target: The Machine.
As the two men walk off, Greer is nearby, talking to his superiors. He informs them that they had to withdraw from Rylatech, but the U.S. government is focused on China rather than Decima. He also reports that he plans to determine the identity of the man who breached their security and eliminate him, while their operation continues as scheduled.