2010 – Day 3191
Finch enters the library on crutches and asks The Machine via a camera if it knew.
2013 - Day 1
The Machine reboots after the Decima virus shuts it down, and dials the pay phone at the New York Public Library. Finch reroutes The Machine's call to the phone near Reese, while Root picks up the call and The Machine makes contact with her. It tells her 3:00 and she says that she understands, and then takes Harold with her. Meanwhile, Reese takes the call and The Machine tells him 4:00. He steps out and shoots at the Decima men, while the phone rattles off more times and tells him to stay. Each time it gives a new time, he shoots and hits a mercenary.
As Root leave with Harold, she tells The Machine to give her abbreviated audio prompts and sound cues. She then follows the directions The Machine gives her and shoots two men through a closed door.
Reese continues to pick off opponents, each one at a different position on a clock, as The Machine gives him their positions. The phone shorts out and Reese hangs up, and he gets a call on his cell phone. The Machine tells him to move now and he leaves with Sam.
Root tells Finch that she's enjoying herself and then asks The Machine how Reese is keeping up to them.
As Reese and Sam leave the library, he explains that he's getting his intel from a computer, the same one that provided Numbers of terrorists to her organization. They find Finch's glasses outside, the ones with the tracker that Reese planted, and he turns to a surveillance camera and tells The Machine to give him Finch's whereabouts. There's no response and Sam assumes that Reese is nuts, When Reese asks for a car they can use, The Machine directs him to a nearby vehicle.
IAB interrogates Carter about the shooting and she insists that the suspect had a weapon. They don't believe her and says that they'll question her again in twenty minutes.
Reese tells Sam about how Root wants access to The Machine to set it free. Reese gets a non-relevant Number on his cell phone but says that it has nothing to do with Finch. A driver parks up in front of them and goes inside, leaving the engine running. As Reese and Sam get in the car, The Machine updates its warning status to Imminent. Reese finally agrees to help and they drive off.
Two Eurotrash mobsters are preparing to kill a man when Reese and Sam arrive and shoot them. Reese tells the man that the police will be there soon and informs Sam that they're done. As they go, they discover that the police have found the car they stole. The Machine directs them to a yellow sportscar and Sam eagerly gets in.
Hersh interrogates a prisoner, Asif, and demands to know about the ferry.
Hersh and his men break into a hotel room and find the Special Counsel, bound and gagged. He complains that they took too long to trace his locators, and Hersh explains that Control thought the Decima situation took priority. Control is worried that Root has full access and the Special Counsel tells them to shut down cell phones and avoid all cameras.
The next morning, The Machine locates Root and Finch in the park. It sends her information on all of the people around her, and she tells it to provide glasses for Finch. The Machine directs her to a man with the same prescription and Root steals the glasses. She tells Finch that they're going to find The Machine.
Terney comes to see Carter and tells her that there's still no sign of the weapon. He advises her to contact her union rep, but Carter says that she recognized one of the unis at the crime scene as a HR man. She tells Terney that she sent Fusco to talk to him. Terney tells her that she could never keep her mouth shut and admits that he doesn't like killing women. He tells her that if she keeps digging and HR will kill Fusco and her kid, and orders her to sit there and take it. Terney's phone rings and he steps outside to take it. Carter clones his phone and listens in as Terney tells his boss that Carter is under control and next they'll take out Elias' right-hand man, and then finally Elias himself. They'll take him out during a prison transfer that night.
Reese follows The Machine's directions and goes back to the library. Finch programmed it not to give him specific directions so Reese figures The Machine has something at the library. He's confident that Finch had his reasons for creating the virus as Greer said, and figures that Root doesn't have The Machine's location either. Reese gets a call from The Machine saying "Ghost Alpha Kilo." He looks up the code for the book, Ghost in the Machine, and finds a photo of Finch and Nathan inside the book. There's a secret panel in the shelf and they open it. There's a safe and The Machine sends the combination. Inside they find photos of women that Nathan helped... including Reese's girlfriend Jessica. He tells Sam that she isn't alive.
Also inside the safe is a map with a route tracing the path of The Machine after the government picked it up. Reese figures that Nathan was looking for The Machine, and narrowed it down to three places. Sam points out that they're all nuclear storage sites, and tells Reese that Root tortured her for information on Daniel Aquino, a nuclear engineer. The man who hired Aquino was Lawrence Szilard.
Root finds Lawrence and says that she has some questions
Finch returns to the library to see Nathan, who says that he's quit. He knows that Nathan is looking for The Machine and points out that he can't access it. Nathan plans to call a reporter and tell him about The Machine, but Finch says that he can't do it. He explains that everyone involved with The Machine is at risk, and that the government is killing the engineers who reassembled The Machine. Lawrence went missing a month ago, and others have died in accidents. Finch warns that if the government knows that he's called a journalist, they'll eliminate him rather than risk it. Nathan says that Finch can't bring himself to trust anyone and asks if he's given Grace his real name. Finch says that he's waiting for the right time, and Nathan asks for the irrelevant list. He asks Finch help him help them, but Finch says that he's trying to help his friend. Nathan tells his friend where he's meeting the reporter the next day and says that Finch should be there.
Root explains to Lawrence that a friend told her where to find him. As Lawrence walks away, Root tells him that it'd be a shame if something happened to his daughter Christine in LA. Finch tells Lawrence how it all started, and Lawrence says that he's apparently the last member of the Northern Lights project.
As Reese gets Lawrence's location from The Machine, The Machine sends him another Number. Sam and Reese drive to a church as a man threatens a newlywed bride, Katie. Reese shoots him, wishes the couple congratulations, and drives off.
Lawrence explains that they were contracted to build a structure in plain sight with enough power for 50,000 people. The government sent in the Army Corps of Engineers and the specs for a nuclear reactor. Lawrence took a look at the I/O and realized that The Machine was practically alive. He realizes that it's speaking to Root. The Machine informs Root that multiple threats are closing in and she leads Lawrence and Finch away. She tells Lawrence that she plans to set The Machine free and he agrees. Meanwhile, Hersh orders his sniper to open fire. The sniper kills Lawrence and fires at Root, and Finch drags her away. She shoots two more men and walks away with Finch, while Reese and Sam arrive and find Lawrence's corpse. She tells Reese to go on and picks up Lawrence's discarded briefcase.
Root steals a truck and gets in with Finch. Reese runs up and calls his friend's name, but Finch ignores him and tells Root that he knows where The Machine is and he'll take her to it. She quickly drives off and Sam figures that Finch had a change of heart.
Hersh continues to interrogate his prisoner about the ferry. Asif admits that he was going to load Semtex on a van, park it next to the Liberty Island ferry, and set it off himself, committing suicide in the process. Hersh shoots the translator and then gives Asif an injection, knocking him out.
Sam tells Reese that she found a baggage claim ticket to Portland in Lawrence's briefcase. One of the three sites is near there and they figure that Root is heading there. They try to commandeer a car and Sam finally ends up firing shots into the street, and the driver quickly gets out.
Root captures a businessman, Chandler, and informs him that they're borrowing his private jet.
Carter calls Reese and tells him that HR is planning to eliminate Elias. He points out that Elias threatened her kid, but Carter explains that Elias had his men paroled so they could watch over his wounded lieutenant. She figures that at least Elias is loyal to his people. Reese tells her to keep her head down as the police close in on them. Reese tells The Machine to give them an extra route and it gives them directions to turn right. There's no place to turn but Sam follows the directions and they go off the bridge. A medevac helicopter team is having lunch nearby and watches as Sam and Reese stagger out of the car and take their helicopter.
Yogorov and Terney take Elias out into the woods to shoot him. Terney says that he learned that Elias' father had two of his men take him into the woods to shoot him, and figures that it's karma. Elias refuses to talk to him and says that at least Yogorov has a legitimate brief with him. He calls Terney an oathbreaker and a worm, and Terney puts the bag back on his head and prepares to shoo him. A masked figure runs out of the woods, shoots Yogorov, and knocks Terney out. The rescuer gets Elias into the car and Elias removes his bag and discovers that his rescuer is Carter. She admits that she doesn't know where they're going.
At the nuclear site in Portland, a containment breach alarm goes off. As they evacuate, Root and Finch casually walk in. They come to a vault door and The Machine informs them that the code has expired. When an engineer comes out and tells them they have to leave, Root draws her gun and orders him to let them in. He does and Root leads Finch in to meet "God." One man, the caretaker, is seated in the middle of a vast empty chamber. Finch apologizes and says that he already set The Machine free. Root begs The Machine to talk to her, and then accuses Finch of lying to her. She prepares to shoot him, but Reese and Sam come in and Sam shoots Root in the shoulder. Finch tells Reese that he had hoped The Machine would be gone.
The next morning, the government learns that Nathan is going to talk to the papers. They know where he's going and figure they have a solution already at hand.
Finch goes to the ferry where Nathan is meeting the reporter. Meanwhile, Hersh drives Asif to the ferry and wakes him up. Asif discovers that he's zip-tied to the wheel and that there's Semtex in the back. Hersh tells the terrorist that he'll complete his mission, gets out, and walks away.
Nathan spots Finch on the ferry and says that it's time for them to face the music. The van blows up.
Reese tends to Root's wound while Finch explains that The Machine could only accept alterations in its programming in response to an attack. He figured that someone would try to take it over and made sure that they did it with his code. Reese realizes that Finch hid a virus within the virus, and that he realized that the people he and Nathan turned The Machine over to were the wrong people. He didn't involve Reese because he hoped that Reese would continue their work.
The alarms shut off and Finch insists that they take Root with them because leaving her would be a death sentence. Hersh and his men come in, guns drawn, and Sam and Reese aim at them. The Special Counsel arrives and tells Sam that he's surprised she turned traitor. She asks what he wants and the Special Counsel asks for a word with Finch. He asks him where he moved The Machine, and Finch says that it moved itself. When the Special Counsel wonders who controls it, Finch says that it controls itself and that it will send Numbers depending on what it feels like sending. The Special Counsel warns him that the country is defenseless, but Finch says that it's only less well-defended. When the Special Counsel asks Finch to help them rebuild or recover it, and gives his word, Finch points out that they gave Nathan their word... and then killed him. Finch leads his people out and the Special Counsel asks Sam if she's choosing the right side. She says that he lied to her as well and leaves.
Finch wakes up in a hospital, covered in blood. A nurse tells him that he sustained injuries to his neck and lower back. As she goes to get help, Finch sees Nathan on a nearby table. The doctors call him as dead and Finch overhears two men calling into report that it's taken care of. Finch borrows a crutch and limps toward the door. Grace comes in, calling for him, and Finch hides behind a screen. She goes to the personal effects table and finds the book with the engagement ring. The two government agents watch the entire room and Finch, realizing that he can't approach Grace without endangering her, limps out.
Later, Finch goes to the library and asks The Machine if it knew. He accesses the non-relevant data and finds Nathan's Number. The clock strikes midnight and The Machine erases all irrelevant data.
The Special Counsel talks to the caretaker, who explains that he apparently received orders from Washington authorized the removal of The Machine. It was removed one node at a time to maintain regular service, and the caretaker has no idea where it was going. He called and confirmed it with the Special Counsel, or so he thought. The Special Counsel receives a call from his superior and assures her that they'll be able to track The Machine. She asks for Hersh and he takes the phone, and he receives special orders to "seal the room." Hersh shoots the caretaker and then his own men. He turns to the Special Counsel, who says "Fair enough," and Hersh shoots him dead.
Back in New York, Reese and Finch take Bear walking. Finch has no idea if they'll receive another Number. He explains that he put the code out to free The Machine, but had no idea what consequences it might have. Finch accepted that someone might get hurt and apologizes for changing things for Reese because of what he did. Reese says that Finch had nothing to do with how he changed his life when he didn't say what he had to, to Jessica. A nearby pay phone rings and they both look at it.
Hersh informs his superior that Research made contact two minutes ago. She tells him to get a team.
Root is locked up at a psychiatric ward. As she walks by a pay phone, it rings and she goes over to answer it. A voice at the other end asks "Can you hear me?" and she smiles and says, "Absolutely."