Two men discuss the death of a Rylatech engineer, Justin Lee, in a fatal "accident." Aware that Monica Jacobs is looking into it, one man tells the other to stop her.
Finch is at Rykers playing his weekly chess game against Elias, and realizes that Elias is toying with him through his moves. When Elias explains that he's trying to learn how to win at a disadvantage, Finch speculates that Elias is referring to the deaths of the DA and Szymanski, and how Peter Yogorov benefited from them. Elias taps the white king and asks Finch who he's playing against, and admits that he doesn't know. Finch warns the crime lord that looks like his loss is foregone conclusion, but Elias tells him that he's not out of the game yet. As the guards take Elias away, the pay phone in the meeting room rings.
Reese is in upstate New York watching a couple, the Coles, while reading a newspaper article about the death of a supposed domestic terrorist... Michael Cole. Finch calls Reese and informs him that they have a new Number. Monica Jacobs is a senior VP at Rylatech, a top server-manufacturing company. While Finch briefs Reese, he passes through the security checkpoint at Rylatech and goes to his new desk in the IT department. Finch informs Reese that Monica is a rising star at Rylatech and could be target of jealous insiders or rival competitors. As Monica and her assistant, Jerome Eckert, walk by, Finch clones her phone. Monica notices Finch's new laptop and talks technology with him, much to their mutual pleasure.
Monica meets with a TOVO executive along with Rylatech's owner, Martin Baxter, and the head of product development, Ross Haskell. When the executive asks why they should work with Rylatech, Monica points out that his company and many others are already using Rylatech servers. She also warns the executive that she knows that their rival Censatek, has been known to give kickbacks to executives who bring them business. After the meeting, Monica tells Martin that she has spies everywhere, and the owner admits that Rylatech couldn't survive without her.
At the precinct house, Carter meets with Tierney, who is in charge of the investigation into Szymanski's and the DA's deaths. He updates her on the case and explains that the only witness, Quinn, claimed that a masked killer came in, shot the two victims and wounded Quinn in the shoulder, and fled. Finch calls Carter and offers his condolences on Szymanski's death, while Cal comes in and approaches Carter's desk. Once she hangs up, Carter tells Cal that she has nothing to say to him until he gives her the name of the CI who tipped him off to the mob money that was used to falsely frame Szymanski. Cal refuses to give up his CI and Carter leaves. Fusco is there and Carter tells him about how she figures that HR killed Szymanski once she cleared her friend of the frame. Fusco promises to do what he can to determine if Cal was involved.
That night, Reese is still outside the Cole home when Finch calls him. Finch is tracking Monica through the RF chip in her ID badge, and speaks glowingly of her expertise. Monica slips out of her offices and breaks into the R&D department, avoiding the guards, and Finch secretly follows her. The VP downloads information onto a flash drive from a laptop in storage and then hides as a security guard comes in. Once the man leaves, Monica leaves and Finch wonders why she's risking her position.
As Finch talks to Reese, Reese hears someone moving up behind him. He turns and finds Sam Shaw, gun at the ready, and signs off on Finch. Reese tells Sam that he thought that she'd come there to speak to the parents of her dead partner, Michael. Reese figures that Sam wanted to tell them that their son wasn't the domestic terrorist that the government claimed. Sam admits that she's watching over the Coles because her ex-organization could eliminate them as well, and tells Reese to pick a different home to watch. As she goes, Reese tells her that a friend once said that even though they walk in the dark, they don't have to walk alone. Sam ignores him and keeps going.
The next day, Finch waits until Monica leaves her office and then goes in and accesses the flash drive. Jerome comes in and demands to know what he's doing, and Finch claims that he's running a security update. Bluffing his way out, Finch says that he's done and leaves.
Fusco finds Cal in the precinct bathroom and demands the name of his CI. He points out that the money from the bodega robbery involving Elias' people never made it into evidence, meaning that either Elias or HR got hold of it. Fusco figures that Cal was in on Szymanski's frame, but Cal says that he knows all about Fusco's past history as a crooked cop. Disgusted, Fusco tells Cal to stay away from Carter and walks out as Tierney comes in.
Monica goes to the computer to pick up some printouts on Justin. Jerome sees her and offers to help, and Monica tells him that she has a last-minute meeting that she didn't put on her calendar. Finch follows her to a park and watches as she meets with Ross. Listening on her phone, he hears Monica tell Ross that she discovered that no one named Lee lived at the address the engineer had on file. Checking further, Monica confirmed that Lee's entire job history was faked. Since Lee worked under Ross, Monica gives him the flash drive and says that she downloaded several encrypted emails from Lee's computer. Once he makes sure that Monica hasn't told anyone else about her suspicions, Ross agrees to look further. As Reese arrives, Finch tells him that they need to figure out a way to download the flash drive info from Ross' computer. Reese bumps into the man as he walks by, pickpockets the flash drive, and gives it to Finch.
Cal meets with Quinn and assures his godfather that he didn't tell anyone that the tip about the bodega robbery money came through Quinn. The narcotics cop admits that he wonders who did give Quinn the tip, since it may have ruined Szymanski's reputation, but Quinn says that it came from a confidential source. The most he will say is that it came from one of Elias' men, and he passed it to Cal so that his godson would get the credit if the Szymanski bust had been legitimate. Quinn figures that a jealous co-worker wanted the bust and is coming after Cal, who thanks his godfather for the help. Once Cal leaves, Simmons comes over and asks if Cal is going to be a problem. His superior says that they'll have to wait and see.
Finch calls Carter and has her look into Lee's fatal car accident, and then returns to Rylatech. As he watches her, he discovers that someone is syncing into her cell phone and uploading a fake phone log. Security men go through Monica's office and when she arrives, Martin and Ross inform her that security found evidence she was going to email confidential designs to their competitors. Jerome, listening in, says that Monica has been acting strangely and going to unscheduled meetings, and Martin tells Monica that she's fired. As security escorts her out, Finch and Reese figure that someone wants her out of the picture... and murder will be the next step.
The next morning, Reese watches Monica as she waits outside Rylatech until Jerome comes out. As she follows him, Finch reviews the information on the flash drive and tells Reese that Lee was a deep-cover spy.
Cal goes to Rykers to see Elias and asks him flat-out if Szymanski was on his payroll. As Fusco listens in via Cal's cloned cell phone, Elias tells the narcotics detective to ask better questions. He asks Cal who benefits from Szymanski's murder and suggests that Cal knows the answer even if he doesn't realize it. Cal is confused and Elias tells him that his own people tried to pay off Szymanski. However, the detective threw the bribe back in their face. Elias tells the narcotics detective that HR used Cal to take Szymanski off the board and tells him to move carefully.
Carter calls Finch and tells him that she checked the black box of Lee's car and found no sign of a collision or of any kind of breakdown that would have driven it off the road. When Finch asks about the condition of the body, Carter tells him that it's disappeared from the morgue.
Simmons meets privately with Quinn and tells him that HR's contacts have spotted Cal at Rykers meeting with Elias. When the cop suggests that they promote Cal to upstate New York and get him out of the way, Quinn tells him to dispose of his grandson and walks off.
Jerome goes to his car and calls his employers, speaking in Chinese. He tells them that Monica is no longer a problem, just as she approaches him and demands to know why he framed her. Reese runs over and grabs Jerome, demanding to know who he works for. Smirking, Jerome tells Reese that there his employers are too numerous to stop, just as a sniper opens fire. The first shot kills Jerome and Reese gets Monica into a car and hotwire the ignition. Finch calls to tell Reese that Lee's encrypted calls were to his father... a high-ranking Community official in the Chinese government.
As Reese drives off with Monica, Finch receives a surprise visitor: Sam. She explains that she traced the phone number he gave her. Finch repeats his offer to give her a job, but Sam shows him a new newspaper article about her dead partner. Due to a CIA leak outing him as an undercover operative, Michael has been cleared of the terrorism charge. Sam figures that Finch hacked into the CIA high-security computer system and faked Cole's record as a CIA agent. While Finch tries to avoid answering, Sam notices a photo of Root on the board and asks Finch what he knows about her. Finch only says that his relationship with Root is complicated, and Sam takes a nearby list of Root's aliases and leaves.
At one of Finch's safehouses, Reese tells Monica what they've learned about Lee. He suggests that Lee was sabotaging her work and assigned Jerome to keep an eye on her. Finch and Bear arrive and they work out that Lee had someone on the inside helping him. Monica figures that it's Ross, the man she took her evidence to, and wants to go to the police. Finch points out that the word of a discredited employee wouldn't accomplish anything and says that they need to get evidence.
Finch hacks the Rylatech firewall using his laptop but discover that the security is too tight to penetrate any further. Monica takes over, explaining that she's familiar with the system, and complains about how she's wasted the last ten years of her life with Rylatech. Once she penetrates the security system, Monica turns the laptop back over to Finch and explains that the people at Rylatech were her family and now they think she betrayed them. Finch manages to discover that the spies inside of Rylatech are using a hidden network, but a hacker at the other end detects his efforts and hacks his laptop, shorting out the battery. Monica suggests that they access the server directly but Finch points out that they need direct physical access. She offers to go in but Reese points out that everyone knows her. Finch gets an idea and asks if she still has her RFID card.
That night, the three security guards at the front desk detect Monica's badge on the premises. When they investigate, they discover that Bear is in the building, wearing Monica's badge. Finch gives the dog an attack order and it chases the security guards into a room. Reese brings Monica in and they access the catalog server in the mainframe room. They install a transmitter and Finch access the system. Noting some anomalous data, Finch keeps working and confirms that there's a heavy data traffic coming in to Rylatech from the company's clients. Monica realizes that someone is using the company's routers to steal information from Rylatech's clients. The hacker spies detect Finch's efforts and he tells Reese and Monica to get out.
Three security guards move in on their position and Reese opens fire. He manages to take out two of the guards and Finch confirms that they're receiving instructions via Ross' office. Reese and Monica head there and find Ross... dead from a gunshot to the head. Martin steps into the room, aims a gun at Reese, and tells him to drop his weapon. The owner insists that he's saving his company, because it went bankrupt during the dotcom bust. His superiors bought him out and now Martin plans to control the future by controlling information. Since Monica and Ross actually believed that the company stood for progress and American principles, they were never brought in to the inner circle. Now Martin will shoot Monica and frame her for Ross' murder. Finch tells Reese that he's already mailed their evidence to the FBI and notified the authorities, and Reese passes the information onto Martin.
As Martin considers what to do next, he receives a call from his superior: Greer. Greer tells him that the time has come and that Martins' family will be provided for. Martin says that he understands, and then shoots himself in the head. When Reese and Monica leave Ross' office, they're surprised to discover that all of the security guards have disappeared. Outside in the car, Finch closes out his server connection... and a payphone next to him rings.
At the station house, Fusco talks to Carter privately and plays her the conversation he recorded between Cal and Elias. Since it proves Cal is innocent, Carter wants to turn the recording over to IAB, but Fusco points out that it wasn't a legal tap. He tells her that the only way they can find out who tipped off Cal is to ask him.
Cal meets Donnie, one of his CIs, and the man gives Cal a tip on a drug deal going down. Donnie walks away and Carter calls Cal. She offers to buy him a drink and talk with him, and Cal is glad to accept. As he hangs up, the dealers run off into a nearby tenement. Cal goes inside after them and chases them into a stairwell... and Donnie emerges from a hallway. He tells the dealers to give him time to get clear, and they open fire on Cal as soon as the CI moves away. Pinned down, Cal calls in for backup.
As Carter finishes up her work for the night, Finch calls to tell her that they have a new Number: Cal. Fusco comes in and tells his partner that they've received a backup request from Cal's last known position. When the two detectives arrive at the tenement building, they find Cal, dead in the hallway. As Carter stares at Cal's corpse in shock, Fusco gently guides her away.
The next morning, Finch and Reese are going to meet Monica. Martin and Ross' deaths have been reported as a murder-suicide, and Rylatech's stock has nosedived. The FBI are investigating the emails mailed to them and replacing all Rylatech servers. When they meet with Monica, she tells them that she's received an offer of employment from IFT, and Finch wishes her well. Once Monica leaves, Reese suggests that Finch is going to miss her and Finch admits that he would if he had the time. He explains that the encrypted code on the data matches the virus that Kara uploaded into the Internet, and originated with a company known as Decima Technologies. Finch believes that the virus was designed with a single purpose: to destroy The Machine.
As Reese and Finch walk away, they're unaware that Greer is nearby. He's equally unaware of them, and is on the phone to his superiors. Greer admits that they had to withdraw from Rylatech, but is confident that the U.S. government is focusing on China rather than Decima. He also tells his people that a single man apparently breached their security, and he plans to identify and eliminate that man. Meanwhile, their operation is continuing as planned.