Finch initiates a surveillance test for the Machine. It is unable to identify him at first, and Root comes in. The Machine confuses her for Fusco, while Reese wires up the precinct cameras. The Machine identifies him as Finch, and points out that it's been two months since the Machine went down and people are dying without them. The Machine continues to glitch on its facial recognition software, and Finch finally is forced to shut down the system to deal with the bug. He assures Reese that they'll get it worked out, and Root warns that they don't have enough processing power. Finch points out that they can't deal with the Numbers, and Root reminds him that the priority is stopping Samaritan and saving the world. He says that the Numbers are the way that they'll know the Machine is functioning properly, and warns Root that she can't go out without the Machine providing her a cover identity. As Finch goes, root gives him a list of things that she needs.
Finch meets Reese in a car and Finch shows his partner Root's list. Reese notes that it's been quiet at work, and Finch advises him to put together a social life. Two policemen come out of a nearby building, and Finch points out that Samaritan is preventing murders. Reese wonders how Finch taught the Machine to be good, and he says by example as they don masks and break into a building to steal computer equipment to get the Machine working.
At the subway, Finch gives Root her sundries and explains that he's built the servers into the subway train. The GPUs that they acquired are the machine's nervous system. Root has tunneled into the government surveillance feeds so the Machine can recover all of the information that it lost, and they reboot the AI. Reese takes to the streets and Finch runs a surveillance test for the Machine. It spots and identifies Reese, but notes that he's responsible for the deaths and disappearances of 62 persons. Finch tries to redirect its attention, having it check people around Reese. It starts identifying everyone in sight, and Finch sees someone who looks like Grace. Root says that it's time to run the Machine full blast, and Finch agrees. He starts the Number-running program, and a nearby pay phone rings. Finch answers it and the Machine recites dozens of Numbers.
Finch eventually tabulates all of the Numbers: thirty different people. Meanwhile, Root has the Machine search for Sam without success. Finch says that he'll set an alert, and warns Root to be careful about how they use the open system. She points out that it almost got them killed last time, but Finch insists on closing the system if the Numbers pan out. Once Root goes to get some rest, Finch checks in with Reese and Fusco. Reese is in on the apartment of a Number who plans to bomb a school, while Fusco is tracking down another man they have identified as victim or perpetuator yet.
Reese busts into the apartment and the Number runs for it. When Reese corners him, he discovers that the Number is a teenager. The teenager says that he called in a bomb threat to get out of a math test. Reese tells him that he's suspended and sends him to his room, and tells Finch that the Machine gave them a false alarm. Meanwhile, Fusco discovers that his Number is an actor in a play who shoots someone. Finch discovers that the Machine is blurring some of the audience members' faces in the surveillance feed, and sees a woman who looks similar to Grace. She gets up and leaves, and Finch tells Fusco to find the next name he sends him. Root realizes that the Machine isn't processing context, and Finch tells her that he's seen Grace twice even though she's in Italy. She points out that Finch hasn't slept and wonders if he's imagining things, and Finch admits that he isn't sure. They run a context check on the two of them and Reese, and it reviews all of the people that they've shot and incidents that they've caused. The Machine determines that they're threats and shuts them out of the system. It then closes the subway train doors, sealing Finch and Root in.
Finch instructs the Machine in human behavior that is unacceptable. He explains about victims and perpetrators.
Finch and Root try to work out what happened, and the pay phone outside rings. Root breaks the window with the case, climbs out, and answers the phone. The Machine gives them another Number, and Finch checks in with Reese. Reese is watching a man, Jeff Blackwell, paint a house. He's an ex-con, and Jeff tells his partner to go on to lunch. Twelve years ago, Jeff killed someone in a DUI. Everything shows that he straightened his life out, and Reese figures that it's another glitch. He assures Finch that they can dismiss Jeff as a threat, but Finch wants more information before Reese leaves. Finch then checks with Fusco, who got the name of one of the mobsters Finch used to instruct the Machine in the difference between right and wrong. When he's unable to access the Machine, Finch tells Reese that the AI can't tell past from present. The new Number is for Laurie Grainger, who is visiting NYC from Tulsa. With time running out, Finch tells Reese to research the Numbers and do triage to determine who needs their help.
At the station, Fusco and Reese check the 27 remaining people. Four are fictional characters, twenty-one are already dead, and five of them were recent suicides. Suicides are on the rise recently and homicides are down, but Reese dismisses it as nothing. Fusco asks if it has anything to do with the sniper who killed Dominic, and Reese looks over at the Samaritan surveillance camera. He tells Fusco to let it lie, and then returns to the six remaining people on the list. Two of them might be in danger: Laurie is one of them. The other man is Gerald Mancini, who has known associations with a gambling ring.
A uni, Mikey, comes over and asks Fusco if he'll be joining them. Fusco begs off and once Mikey leaves, Fusco figures that Reese is jealous because Mikey didn't say anything to him. He suggests that Reese learn about his co-workers and figures that his partner is lonely. Fusco suggests that Reese go bowling with him, but Reese tells him to check Gerald while he takes Laurie. Fusco hands her over to Reese, who says that he's just the guy she needs.
Root disconnects the wireless receiver letting the Machine control the door. She suggests that they reboot the Machine in safe mode. The Machine, monitoring them, employers countermeasures and sends feedback through Root's cochlear implant. Root clutches at her head in pain and warns that the Machine doesn't want them to do the reboot, and points out that the Machine is scared of them. Finch tries to talk to the Machine, and it brings up a live feed of them showing that they're threats.
At the station, Laurie tells Reese that her friend is out of town and she's staying at her place. She heard a noise at the window, grabbed everything valuable, and got out of there. Laurie asks Reese to take a look, but Finch calls and says that they need his help since the Machine has turned on them. Reese tells Laurie to stay there and leaves, but she goes after him.
As Reese heads to the station, he tells Finch to get out. Finch refuses to leave Root, who will be killed if she goes above ground. Laurie comes up behind Reese and shoots at him. Reese takes cover and shoots back, and tells Finch that he's the victim. He realizes that she has special forces training, and Root confirms that Laurie has an entire false digital life. Reese warns that he can't come to the station without giving them away, and Finch tells her to capture Laurie and find out who she works for.
Laurie stops shooting and Reese goes over to investigate. She has abandoned her bag, and Reese realizes that she had a larger gun in it... just as Laurie steps out and opens fire on him with a semi-automatic.
Finch approaches the monitor and the Machine sends more feedback through Root's implant. He insists that they help people, but the Machine brings up records of Root killing someone. Finch says that Root has changed because of her intervention, but the Machine brings up more recent videos. It then brings up video of Finch attacking the Machine, and he realizes that the AI thinks that it's monsters.
Fusco calls Finch and says that Gerald has huge gambling debts causing wedding issues., and it might turn violent. Finch tells him to handle it, and then suggests that the Machine sent Laurie after Reese. He wonders what happens if it comes down to the Machine or them, and Root points out that the Machine is their only chance of survival. Finch checks with Reese, who sees Laurie running into a nearby mall. He goes in after her but loses her in the crowd.
In the station, Root grabs a canister of anesthetic and instructs Finch in how to intubate her. Once she's unconscious, the Machine won't have any leverage over Finch. Root tells him to go for the root directory. The Machine will shot him out, but he'll find a way into the system. If that doesn't work, Root tells Finch to talk to the AI. Once Root is out, Finch goes back to the monitor and overrides the lockout. He brings up surveillance of Laurie, and the Machine admits that it hired her to kill Reese.
Reese spots Laurie and shoots, and she returns fire.
Finch asks the Machine to call off the hit, and reminds it that he taught it. The Machine brings up video of Finch explaining that it has to separate the bad people from the good. Finch admits that things were clear then, but now black and white have dissolved into grayscale. He tells the Machine that he was wrong, and he's no hero: just someone doing the best he can. Finch apologizes for everything and says that he, Root, and Reese did the best they could.
The Machine brings up a surveillance feed of Reese and says that certain things are unforgivable. It lists out everything that Reese has done, and Finch says that his friend is fighting hardest to be good. He then contacts Reese and tells him that the Machine hired Laurie to kill him. The Machine shuts off the feed, and Finch tells the AI that they can work together. He promises to never hurt it again, and the Machine says that he's hurting it now. Finch asks what day it is, and it explains that it is constantly reliving the 42 times that Finch shut it down and rebooted it. He realizes that the Numbers are the Machine's anchor in time, and shows it all of the cases of the people that they saved.
Reese is out of ammo and says that he'll have to call for backup. He tries to reach Finch, who is dealing with the two hitmen that have come for Gerald. He kneecaps the two men and realizes that he left his cell phone in the car.
When Fusco doesn't answer his phone, Reese realizes that he's on his own. Laurie moves in, while Finch finishes by showing the Machine Grace and explains that it helped them save her life. He says that the Numbers will help the Machine count the days, and insists that saving the lives is a pure good. Finch promises to do the best that they can. The Machine reassesses all of the contextual data and recognizes Finch as the admin. It apologizes, and Finch asks it to call off Laurie. The Machine says that she was paid in advance. Finch tells Reese to run for his life, just as Laurie closes in on him. He gets behind her, disarms her, and trains the gun on her.
The next morning, Finch takes down the photos of all the Numbers. He goes to the monitor and asks the Machine to show him Grace. It brings up a surveillance feed of her and Finch asks the AI why it showed it to him before. The Machine has no idea what he's talking about. Finch thanks the Machine and leaves with Root.
Finch and Root go to a park after the Machine reestablishes Root's cover. She says that they need the system open for the time being, and Finch agrees. They join Fusco, who is reading a newspaper that shows him as a hero for saving Gerald and his family. Reese arrives wearing a bowling uniform, and Root looks at the people enjoying themselves despite the fact that they're at war. Finch says that the Machine seems sane again.
Jeff goes to the employment center and asks for something permanent. A woman, Mon, tells him that they have just the thing for him. She knows about his record and says that the position is his if he wants it. Jeff offers to fill out a personality test, but Mona assures him that he has so much potential and figures that he needs a purpose. The Machine watches as Mona says that it's time to put Jeff back to work... and flags them both as threats.
Written by Gadfly on May 10, 2016