Reese meets with Finch at a warehouse to show him how to use a firearm. Finch refuses, and Reese warns his friend that he won't be around forever. A nearby payphone rings.
CEO Sulaiman "Saul" Khan is sleeping at home when his assistant Kelly Brewer runs in and tells him to pick up his phone. She turns on the TV and a reporter explains that the company was hacked and all of the records exposed. The leak shows that Saul was embezzling company funds, and Kelly warns that the board is moving to fire him. Saul tells her to call Mark Lee and have him stall. IRS agents arrive at the front door and Saul tells Kelly to buy him some time while he gets to the board meeting and fixes things.
Reese is watching as Saul leaves the building via a side entrance. He checks in with Finch, who explains that Saul is the CEO of Castellum Security Incorporated. Saul pioneered computer antivirus software and now owns the biggest software company in the world. He's worth billions, but his finances took a major hit during the stock market flash crash engineered by Samaritan. Saul's anti-virus software is installed in 86% of computers around the globe. Reese has been unable to bluejack Saul's phone because of his security software, and Finch concedes that whoever hacked him is very good. Meanwhile, Reese bluejacks Kelly's phone and watches as Saul discovers that the smart key for his car has been voided. When Reese suggests that Root help, Finch says that they're not on the best of terms.
Root is at a restaurant watching two men meet. One of them hands off a briefcase to the other and assures him that it's secure. Meanwhile, Root takes out a gas mask and hits a remote, and gas pours into the restaurant. Once everyone is unconscious, Root walks out with the briefcase.
Saul takes a taxi to Castellum and Reese follows him in. His phone rings and Finch hacks his wife Linda's phone. Linda is furious that Saul didn't delete the pictures from Cabo, which show him and his mistress. Finch confirms that the Khans have been seeing a marriage counselor for the last month. She's furious that her reputation has been ruined, and hangs up on Saul.
In the board room, Joseph Nicasso is calling for a vote against Saul. Reese has contacted Zoe and she's attending the meeting, passing the information onto Reese. Saul arrives and Zoe says that the board hired her to clean up the mess. Nicasso informs Saul that the vote was unanimous and he's out. He admits that he wrote the emails, including one insulting Mark behind his back, but insists that he was angry and wrote it in private. However, he denies embezzling the money and insists that he's been setting up. Nicasso says that three teams of analysts have confirmed the charges, and Saul accuses him of trying to take his software since he joined Castellum. Finch checks the malware and discovers that the threat came from within.
Nicasso tells Saul that he lost focus and diverted money into secret side projects, driving Castellum into bankruptcy. Saul insists that Nicasso has been taking the company and its software backward in design and efficiency, and his work in digital immunization technology will take Castellum to a new level. Nicasso says that the hacked data shows that Saul embezzled $400 million to finance his biotech, and Saul's leaked medical records show that he's bipolar. He has a security guard escort Saul out, and Saul storms out. Finch warns Reese that there's no telling how Saul will react.
Saul goes back to his apartment and finds workers taking all of his stuff. Shocked, he calls his lawyer and asks for Ira Waxman. The secretary, Mandy, informs Saul that they've dropped him as a client. Reese and Zoe watch as Linda comes out and says that the IRS is coming after her as well, and they're through. While they watch, Zoe warns Reese against settling down with Iris. He wonders if she's jealous, and Zoe warns that Reese knows how it ends. She wonders why the hacker went after Saul but not Castellum, and points out that someone set out to take out Saul without harming the company. Zoe figures that it's personal, and then walks away.
That night, Saul goes to Kelly's apartment. He blames himself for losing focus, and Kelly advises him to fight back. She then gives Saul the gun he requested, and he says that he's sure that Mark will show up just to see him squirm. Saul thanks her for her help and Kelly assures him that she'd do it anytime.
Two men follow the GPS tracker on the case that Root stole. Meanwhile, she's in a hotel room trying to pry it open and remove the tracker. The Machine doesn't tell her, and Root uses a lamp cord to short out the tracker. The men break down the door and then check the access door to the adjoining room. Root is ready for them and shoots one, and uses the case as a shield against the other man before knocking him out.
Saul waits at a cheap bar for Mark, while Reese sits down the bar. Finch admits that Mark has plenty of motive to bring Saul down. Mark comes in and Reese bluejacks his phone. Saul destroys his friend's phone and asks Mark to trust him. He points out that the hacker didn't go after anyone else, and asks Mark to go to the meter room for him. Saul wants to see the gauges and figure out how his anti-virus software was gutted. Mark figures that Saul is holding something back, and the former CEO says that a few weeks ago the entire facility went dark. The money to pay the accounts was used to pay for 25,000 barrels of diesel. Saul warns Mark that the stock market flash crash was targeted at him, and every equity he had was wiped out except for his Castellum stock. Finch confirms that Saul is telling the truth, and realizes that Samaritan is the only thing powerful enough... just as Saul tells Mark that an AI is after him.
A man at the bar is on his iTouch, unaware that Samaritan is using it to listen in on Saul's conversation. Meanwhile, Saul tells Mark that the attack was more dangerous than anything he's seen. Mark figures that whether Saul is right or wrong, it's best for him to stay away from him. He walks out and Reese realizes that Saul stole Mark's employee ID badge. Finch warns Reese that there's no way to protect Saul if Samaritan is the perpetrator, but Reese goes after Saul.
Later, Saul breaks into Castellum and enters the meter room. Samaritan monitors him and notifies a guard, but a masked Reese knocks out the man before Saul can notice. Reese then follows Saul in and takes photos as he checks the power gauges. As Reese moves in, Finch warns that the NYPD have arrived and Samaritan will see through Reese's cover. Reese has no choice but to leave, and the policemen arrest Saul.
At Decima, Greer offers Martine a cigar to celebrate the fact that they've pinpointed Saul. He admits that Saul has forced their hand, and tells Martine that Samaritan wanted to handle him personally. Martine wants to go after Root, and Greer agrees.
At the station, Fusco discovers that Saul was transferred to Rikers and passes the information on to Reese. Reese insists that Fusco go with him and get Saul out, and Fusco reluctantly agrees despite the captain's orders. Finch warns that if he hacks the police database then Samaritan may detect him.
At Rikers, the guards inform Saul that the records show he already had a phone call. They process him and escort him to a cell past Fusco. Fusco flashes his badge and says that Saul is his witness in a joint case with the Feds. The clerk checks the computer and says that Saul has a half-dozen open felony warrants. Fusco goes out and tells Reese, and then hears something banging in the trunk. Reese says that it's Plan B and Fusco heads back to the station.
The guards throw Saul into general holding, and he spots a security camera. One of the prisoners receives an anonymous call offering $50,000 to kill Saul. The man walks past Saul, eying him carefully.
Finch warns Reese that Samaritan has cut the security feeds to the cell block. Reese goes in wearing a guard's uniform, and takes out the prisoners just as they grab Saul. He gets Saul out before the security feeds come up, and drives across town in a stolen transport van. Finch tells him to stick to the shadow map, while Saul recognizes Reese from the bar. Samaritan reroutes the lights, forcing Reese to switch to a side street, and then raises the bollards ahead. Reese climbs out of the wreck just as a van pulls up. It's Root, who offers him a ride.
Root takes Reese and Saul to a safehouse and Finch arrives. He warns that the safehouse won't stay safe for long, and Reese suggests that they recruit Saul. He doesn't think that they'll convince Saul the way that they did Simon Lee. Saul wakes up and tries to run, only to discover that he's manacled to the table. He assumes that Samaritan sent them, and Finch offers to release him when he answers their questions. Reese asks why he needed to see the meters, and Saul explains that the company's power usage had increased tenfold. He figures that all of the computer-related activity was caused by an AI, and that his company was hijacked so the AI could build a prototype without him. Reese reminds Finch of Maple, NY, where Samaritan was building transponders. Saul realizes that they believe him, while Root uses Finch's laptop to locate the off-site IP address that was used to hack Saul's computers. The area is covered in woods, blocking overhead imaging, and Root suggests that they go and investigate.
Reese and Root are soon packing a SUV with guns and C4. Saul insists on going with them and Finch gets in the SUV with them. They drive to the coordinates but find no sign of activity. As they look around, Root picks up digital images on her cochlear implant. She passes the coordinates on to Reese, who aims with his sniper rifle and takes out each of the security cameras. Root then finds metal doors beneath the snow, revealing a stairway leading down.
As Samaritan sends teams toward the site, the group enters the underground facility. They find a man at a computer console and take him prisoner, and he explains that he's running diagnostics on antivirus software that is scanning all over the grid. Finch accesses the systems and discovers that all of Castellum's servers have been hijacked and Samaritan is running a global search. Saul spots a line of code just as Root hears men approaching. She says that they have to get out, and Reese gives Finch a gun and tells him to stay close.
The team returns to the surface, and Martine and her agents open fire on them. Meanwhile, Saul says that the code he saw was his software, only elevated. He demands that Finch tell him what's going on. Root spots Martine and goes after her, and Finch yells a warning to Reese as a Decima agent comes up behind him. Reese spins and shoots the man.
Root and Martine both run out of ammo and fight hand-to-hand. After a brief battle, Root takes Martine down and starts strangling her. Meanwhile, Finch tells Saul that his isn't the first life that Samaritan has ruined. A Decima agent moves in and Reese shoots him... and Saul escapes in the confusion. More agents move in and Reese tells Root that they have to go.
Later back the subway station, Root tells Reese that he should have let her kill Martine. He says that it won't bring Sam back, and then admits that she's right. Reese notices the stolen case and asks what's inside it, and Root admits that the Machine hasn't told her yet. Once he's gone, the Machine sends Root the case's combination. She opens it and finds a Faberge egg inside. The Machine sends her a message and she smashes it against the wall and then puts the case on a shelf.
Reese and Finch take Bear out walking, and Reese asks what Saul saw. Finch explains that he used unique code to create The Machine. Samaritan knew that and started a search for unrecognizable code, using software that The Machine wouldn't detect because Saul's antivirus software was already installed on millions of computers. Finch warns Reese that Samaritan will eventually find its counterpart. As they talk, a pay phone rings nearby.
At Decima, an agent brings Saul to Greer and Martine. Greer explains that he's has finally tracked down the Machine, but it's not on any network machine in the world. He tells Saul that there are two AIs, and Saul asks to see it. Greer agrees and shoots him, and Saul looks up at the screen as it registers him as a threat terminated.