2013 - Day 4111
The Machine tries to review the events leading up to Decima uploading a virus into its programming.
Reese calls Finch at the library and asks if he has a new Number, since it's been ten days since The Machine last gave them a number, and the virus monitor is counting down to 20 hours remaining. Finch tells him that The Machine is active but can't communicate with them. Reese is listening in on the police band frequencies and picks up a call about a murder.
Carter arrives alone at the scene of a triple shooting because Fusco is working another case. Terney is there and tells her that two of them are Elias' men and the other one is an innocent. They figure that it's Elias' competitors, the Russians. As they check out the crime scene, Terney assures Carter that he'll do whatever he can to help her find Cal's killer. Carter spots Reese standing near an alley and goes over to talk to him. He offers his condolences about Cal's death, and Carter wonders why Reese and Finch are no longer stopping murders. Reese admits that a situation has come up. She asks him to hurry and admits that the Russians are worse than Elias.
In Washington, the Special Counsel is on the phone to Control, warning him that they haven't received any Numbers in a week. The undercover Root brings the Special Counsel tea and leaves, and the Special Counsel tells his superior that they've connected the chip in Corwin's body to Decima. He figures that Decima is trying to eliminate The Machine. Root comes back in and draws a gun on him, and demands answers to her questions.
The next day, Finch is walking Bear and looks up at a surveillance camera. A nearby payphone rings and Finch answers it. The Machine gives him a series of names and Finch goes to the library. He explains to Reese that the Number is Ernest Thornhill, the CEO of a data entry company. Thornhill has recently bought several payphone companies in upstate New York. Finch says that it will take time for him to hack Thornhill's database so Reese goes to pay him a personal visit.
Finch goes in undercover as a technician while Reese tells Thornhill's secretary, Claudia Sugarman, that he has an appointment. She says that Thornhill is traveling and didn't have an appointment, and Reese says that he'll contact the CEO later. Meanwhile, Finch checks a garbage can and discovers that the data entry assistants are typing in code from dot matrix printers. They are taking data and transferring it from one computer to the next, and Reese figures that it may be a front.
Root calls Finch as he checks the company computers and asks what he did to The Machine. She wonders why it isn't defending itself but Finch refuses to talk to her. Root suggests that they work together and warns Finch that Reese can't help him. When Root mentions Thornhill, Finch wonders what she knows and she offers an exchange of information.
2010 – Day 3177
Finch goes to see Nathan and notices that he has several pill bottles sitting around. He explains that they've been putting the company together since they gave the government to The Machine, and Finch says that he wants to make a personal change. Finch explains that he's met a woman, Grace, and wants to get Nathan's opinion on the book that he bought her. It has an engagement ring inside and Finch worries about how to tell her the truth about who he really is. Nathan points out that there are legal implications due to Finch's activities in his youth, and Finch suggests that they hire some lawyers. However, Nathan warns him that their friends in the government may not appreciate that Finch was his silent partner. Finch says that they're done with that, and Nathan offers a toast to the first day of his new life. He goes to get some champagne and his cell phone rings. Finch sees it and discovers that Nathan is receiving a SMS system message.
2013 – Day 4138
Back at the library, Reese and Finch wonder why Root is interested in Thornhill. According to the files, Thornhill opened an account six months ago and it went from one penny to $20 million. After that, he started buying up payphone companies. According to Thornhill's credit card, he recently rented a car to pick him up at JFK, and he'll be back that day. Reese says that he'll go to greet the CEO and promises not to let Root get Finch again.
Reese takes a motorcycle to JFK and waits on the only route out. Finch tracks the car GPS and Reese spots him, but notices a SUV pull over nearby. A man gets out with a cell phone and uses it to direct a drone toward Thornhill's car. Reese shoots at the man, forcing him to drop the remote, but the drone slams into Thornhill's car and explodes. The killer drives away and Reese goes to the car, only to discover that the passenger section is empty.
Back at the library, Finch checks the phone the killer used and determines that it has an electronic signature similar to the virus targeting The Machine. Carter calls to tell them that the driver is in stable condition, and that according to her investigation, none of Thornhill's employees have ever met the man. Once Carter hangs up, Reese tells Finch that Thornhill is a ghost that doesn't exist. Finch has a different theory and explains that he checked the only photo that they have of Thornhill. It's a composite, and two days ago Thornhill sent an email from a public location. However, according to the security camera there was no one there. The email was encrypted using an algorithm that Finch developed... for The Machine. Finch realizes that Thornhill isn't a spy: he's a fake ID created and maintained by The Machine.
2010 – Day 3178
Finch meets Grace in the park and she paints a portrait of him. He asks for her phone and locks it in his case, and suggests that they go somewhere more private. The Machine watches via nearby cameras as Finch gives Grace the book and then proposes to her. She accepts and they kiss.
2013 – Day 4138
Finch explains that he has no idea why The Machine created Thornhill, and insists that he took precautions that it wouldn't get creative. When Reese wonders why The Machine needs a fake ID, Finch figures that it needs to meet the residency requirements to own a payphone. As they talk, Finch sees an anonymous request on his computer asking to meet. He tells Reese to check out Thornhill's apartment and see who else goes there looking for Thornhill. Once Reese leaves, Finch calls 911.
At the station, Carter checks up on Thornhill's rental car. She calls Reese, who is at the apartment, and asks why someone rented a car even though there was no passenger. He tells her that they have it under control and suggests that she spend her time pursuing leads on Cal's death. Sam Shaw slips in behind Reese and demands to know what he's doing. She explains that she's there hunting Root.
Finch goes to the designated meeting spot, which is near Grace's apartment. He watches as she leaves her apartment, and Root comes up behind him and says that she's lovely. She says that she doesn't have any intention of hurting Grace, and says that at midnight when the virus reaches 0 that night, The Machine will call a payphone. Whoever answers it will receive full administrative access because of Finch's original coding. Root wants to stop Decima from controlling it and save The Machine. She tells Finch that if he doesn't help her then she'll kill Grace. As she starts to walk away, Finch agrees but tells her that they're not going to kill anyone.
Simmons calls Terney and tells him that the boss wants Carter eliminated. Terney goes over and tells Carte that he has a lead on Cal's killer, and she goes with him. The Machine, watching on the station cameras, tries to call Finch from a payphone as he walks by. Root drags him away, saying that they don't have time to deal with whatever emergency The Machine is reporting.
Sam tells Reese that Root infiltrated the Program. Before Reese can call to warn Finch, policemen bust in and Sam slips out the window, leaving Reese behind.
2010 – Day 3178
Finch is walking downtown and leaving a message for Nathan about the good news he has. As he hangs up, Finch sees Nathan leave a building, check his phone, and then walk down the street. Finch follows his partner, tacking the GPS in his cell phone, and watches as Nathan enters an abandoned library. Once he's inside, Finch follows him in and asks what it is.
2013 – Day 4138
As they walk down the street, Root speculates that Finch programmed The Machine with a God Mode program to give the creator access in case of a system crash. She figures that Decima wants access and went after Thornhill because he was buying every payphone in Manhattan. Root wonders why Finch left it vulnerable but he refuses to answer. When she asks how vulnerable it is, Finch says that whoever answers the call will have unfettered access for 24 hours. He refuses to tell her which payphone it will call and is confident that Decima can't know which one. Root points out that Decima's people are guarding every payphone in midtown so she figures it's somewhere around there. They can't go to the true phone without tipping their hand, but Root tells him that they don't need a plan because Thornhill already has one.
When Reese is brought in to the station, the police let in his lawyer. It's Sam, and she warns him that Finch doesn't want to be found. Sam plays back Finch's 911 call warning them that Reese was breaking into the apartment. She asks Reese if he can track Finch, and he admits that he put a tracking bug on Finch's glasses. As they talk, Sam removes her scarf and dips it in a pitcher of water. She then removes two guns taped to her back and tosses her briefcase out into the hallway. It explodes and they walk out, using the scarf for a mask.
Root breaks into Thornhill's company and deduces that The Machine created Thornhill to protect itself. As they go into the office, all of the dot matrix printers start up. Root tries to work out what's going on and realizes that the code being transferred is The Machine's memories. Finch tells her that when he was building it, he realized that it was imprinting on him like a child with a parent. However, he needed a machine, not a person. Finch explains that every night The Machine deletes its own identity programming. Root realizes that they're standing in an external hard drive that The Machine created. Every night they type its memory code back in, but the process has all but crippled it. To save The Machine, they have to intercept the call.
Carter and Terney drive to a house with two other officers. Terney takes Carter around the back alley and prepares to shoot her. However, the drug dealer runs out, sees them, and goes for his gun. Carter shoots him and Terney has no choice but to call for backup.
Reese and Sam track Finch's GPS locator to Thornhill's company. Decima mercenaries open fire on them and Sam and Reese take them down. Greer is standing at a computer and addresses them both name. Reese orders him to explain how to stop the virus, but Greer refuses. He explains that he found it on the laptop that Reese and Kara retrieved from China. If Reese kills him, Greer warns that he'll never find out who wrote it. He tells Reese that the man who sold the laptop in the first place is Finch. He admits that he hasn't been able to identify Finch yet and looks forward to meeting his acquaintance. More Decima mercenaries run in and open fire. Sam and Reese take them out, but Greer escapes in the confusion.
2010 – Day 3178
Nathan figures that Finch doesn't trust him, and reminds him that he bought the library and fourteen others like it. Finch notices a board with photos of people on it, and Nathan explains that he saved five people... and lost seven. He tells Finch that he couldn't stop thinking of the people that Finch said were irrelevant. Nathan just gets the Numbers and never knows if they are the victims or the perpetrators. He does believe that The Machine wants him to know the information.
Finch warns him that whatever precautions he took won't last for long if the government tries to track him down. He starts to shut down The Machine, but Nathan asks if he's willing to look the next Number in the eye and tell them that they're irrelevant. Finch says that he'd say that the greater good is at stake and tells Nathan that he's sorry, but people die and they can't save all of them. He shuts down The Machine and walks away... unaware that the next non-relevant Number was Nathan's.
2013 – Day 4138
Greer checks with his people and informs them that the virus has identified the exact phone that The Machine will call: The New York Public Library.
Finch takes Root to the public library and points out the phone that he knows The Machine will use. Two Decima mercenaries arrive, cutting them off. However, Root goes to the juncture box, tasers the man guarding it, and tells Harold to intercept the call. She insists that she wants to save The Machine from Decima as well as what Harold did to it. Once they have access, she'll find out its location and go to save it.
IAB detective Ed Solis arrives at the crime scene and tells her that she's under arrest. Terney claims that the suspect didn't have a gun, and there's no trace of the weapon on the body.
Reese and Sam enter the library and open fire on the Decima mercenaries. Root sees him and goes back to Finch, while Reese takes one of their phones and confirms that there are more mercenaries on the way.
The clock reaches midnight and The Machine shuts down and then reboots. It goes into debugging mode and calls the admin. The phone rings and Root goes to answer it. However, Finch redirects the call to the phone booth near Reese. He then sends a text message to Reese saying that it's for him. As he goes to answer it, Root tells the caller at the other end that she understands. She puts in an earbud and then goes to get Finch and tells him that the fun is just beginning.
Reese answers the phone and a computer voice asks if he can hear it.