2010 – Day 3191
Finch hobbles into the library, sits down at the computer, and asks The Machine if it knew.
2013 - Day 1
Finch splits the incoming call from The Machine to two payphones in the New York Public Library. Root takes one call and Reese takes the other, and it talks to them separately. The Machine says "3 o'clock" to Root, and she says that she understands. She then grabs Harold and leaves.
Down on the main floor, The Machine tells Reese "4 o'clock." He turns and shoots a Decima mercenary, and The Machine gives him more times. Each time, he shoots a different man.
As Root leaves with Harold in tow, she tells The Machine to use sound cues rather than audio prompts. It emits different tones, indicating which direction to fire, and she shoots two Decima men through a door.
Reese continues to pick off opponents, following The Machine's directions via clock positioning. The Machine shorts out the payphone and then calls Reese on his cell phone, telling him it's time to move, and he leaves with Sam.
As they take the elevator out, Reese asks how John is keeping up with them. Finch says that he doesn't know, but Root says she wasn't talking to him. However, she gets no response from The Machine.
As they leave the library, Reese tells Sam that the Northern Lights "research department" is an intelligent computer and providing him with his intel. They find Finch's glasses outside and realize that he no longer has the GPS locator that Reese was using to track his friend. Reese asks a surveillance camera for Finch's whereabouts but gets no response. He asks for a car and The Machine directs them down the street.
At the station, IAB interrogates Carter about the shooting. She insists that the suspect had a gun but they don't believe her and leave her alone for a brief break before they return to questioning her.
As Reese explains how Root wants to set The Machine free, The Machine sends him a non-relevant phone number. He says that it has nothing to do with Finch just as a man pulls over in a car, leaves the engine running, and goes inside. As Reese and Sam steal the car, The Machine says that the non-relevant's danger status is imminent. Reese reluctantly agrees to help and they drive off.
Two mobsters in the back of a semi are preparing to kill a prisoner when Reee and Sam arrive. After they gun down the mobsters, Reese tells the man that the police are on the way and they go back to their stolen car. The police have already found it and Reese asks The Machine for a new car. It sends them to a storage building and they find a yellow sports car waiting for them. Sam gives Reese her gun and takes the wheel.
Hersh interrogates a terrorist prisoner, Asif, and asks him what their plan was for the ferry.
Hersh and his men trace the Special Counsel's locator to a hotel room and find him tied to a chair. When the Special Counsel complains that they took too long, Hersh tells him that Control ordered them to focus on the Decima situation. They know that the Special Counsel's executive assistant was actually Root and they plan to bring her in. The Special Counsel tells his men to shut down their cell phones and avoid all cameras.
The next morning, Root and Finch go to a park and she receives a data feed on everyone around them from The Machine. She tells it to provide Finch with glasses and it gives her directions to a man with the same prescription. After Root steals the glasses from the man's backpack, she tells Finch that they're going to find The Machine.
Terney visits Carter in the interrogation room and suggests that she contact her union rep. Carter tells him that she recognized one of HR's people at the crime scene and figures that he took the gun. When she says that she sent Fusco to talk to the man, Terney complains that she couild never keep her mouth shut. He tells Carter that if she doesn't drop the case against HR and take the blame for the shooting, the organization will kill her, her son, and Fusco. As Terney leaves to take a call, Carter clones his phone and listens in. Terney tells his boss that he has Carter under control. He plans to dispose of Elias that night during a prison transfer.
The Machine instructs Reese to go back to the library to find out where it is currently located. Reese figures that The Machine sent him there because it's programmed so it can't give its location directly to either him or Root. When Sam wonders about the virus that Greer claimed Finch created, Reese is confident that Finch had his reasons for it. The Machine sends a book code and Reese and Sam find it on the shelves. It contains a photo of Nathan and Finch, and there's a safe hidden behind the shelf. Inside it are photos of the first non-relevants that Nathan tried to help... including Jessica, Reese's fiancee. Sam realizes that Jessica meant something to him, and Reese tells her that Jessica isn't alive. There's also a map showing three possible locations that Finch and Nathan determined might house The Machine. Each of them is a Federal nuclear storage site, and Sam points out that Root tortured her for information on Daniel Aquino, a nuclear engineer that Control had murdered. The man who hired Aquino was Lawrence Szilard.
Root gets directions to Lawrence, who is at the park, and approaches him.
Finch goes back to the library to see Nathan and warn him that he can't try and access The Machine. Nathan tells his friend that he's going to tell a reporter about The Machine, but Finch warns him that the government is killing everyone who has any connection to The Machine and its shipment. Lawrence, the head of the reassembly project, went missing a month ago, while all of his co-workers have met with "accidents." If the government learns that Nathan is going public, Finch figures that they'll kill Nathan as well. Nathan says that Finch can't bring himself to trust anyone and wonders if he's given Grace his real name yet. Finch says that he's waiting for the right time, and Nathan asks him to help the non-relevants, but Finch only wants to help his friend. Nathan tell him that he's meeting the reporter at a ferry the next day and invites Finch to join him.
Root has a photo of Lawrence's daughter Christine, hiding in LA, and hints that she could be in danger if he doesn't cooperate with her. To convince him that they know what they're talking about, Finch describes how the government would have shipped The Machine cross-country. Lawrence admits that he was the head of Northern Lights and that he's the last surviving project member.
The Machine gives Reese Lawrence's current location, but also sends him a new Number. Sam drives to a church where a jilted man is preparing to shoot a newlywed couple. Reese kneecaps the man, offers his congratulations to the couple, and drives off.
Lawrence explains that the government gave him the plans specs for a nuclear storage facility and the Army Corps of Engineers to build a structure in plain sight with enough power for 50,000 people. He caught a glimpse of The Machine and was impressed with its elegance, and realizes that Root is in contact with it. The Machine tells Root that multiple threats are closing in and she starts to lead Finch and Lawrence away. As Lawrence agrees to help Root free The Machine, Hersh's sniper takes him out. Root and Finch escape, with Root shooting two of Hersh's men as they go. Reese and Sam arrive and find Lawrence's corpse, and Sam grabs the briefcase. They go after Root, who has stolen a truck. When Reese calls Finch's name, Finch ignores him and tells Root that he'll take her to The Machine. She drives off while Sam and Reese can only look on.
Hersh continues interrogating Asif until he admits that he as going to drive a van filled with Semtex to the LIberty Island ferry, and then detonate it personally. Hersh shoots the translator in the room and then injects Asif with a sedative, knocking him out.
Sam shows Reese a Portland baggage claim ticket that she found in Lawrence's briefcase. One of the three nuclear facilities is near there and they commandeer a car. Meanwhile, Root tracks down a businessman and orders him at gunpoint to take them to his private jet so they can fly to Portland.
As they head for the airport, Reese calls Carter to see what she's doing. She tells him about HR's plan to kill Elias and admits that at least the crime lord is loyal to his people. Reese tells her to keep her head down and hangs up as the police close in on their stolen car. The Machine gives them to turn off in a few hundred years, but there's no exit. Reese has Sam do it anyway and they crash the guard rail and land near a helipad. The medevac team is having lunch and stares in surprise as Sam and Reese get out of the wrecked car and take their helicopter.
That night, Yogorov and Terney take Elias out into the forest to kill him. Terney figures that it's karma since Elias' father did the same thing to his son when he was a teenager. Disgusted, Elias says that Terney is an oathbreaker and that Yogorov at least has a legitimate case for shooting him. Terney puts a bag on Elias' head and prepares to shoot him, but a black-clad figure arrives and shoots Yogorov. After knocking out Terney, the newcomer takes Elias to a car and gets him in. When Elias removes the bag, he discovers that his rescuer is Carter. When he asks where they're going, she says that she doesn't know.
At the Portland nuclear facility, Root sets off a containment breach alarm and then walks in with Finch. They go to the primary storage vault and The Machine informs Root that the code has expired. An engineer comes in to tell them to evacuate, and Root forces him at gunpoint to unlock the vault. She goes in with Finch to meet "God," and he warns her that she might be disappointed. The vault is one huge room... with a caretaker sitting a table and nothing else. Finch tells Root that he already set The Machine free, but she doesn't believe him and prepares to shoot him down. Reese and Sam arrive and Sam shoots Root in the shoulder. When Reese asks him if he knew The Machine would be gone, Finch admits that he only hoped it.
The next morning, Control learns that Nathan has contacted a reporter and where he's meeting them. They realize that they already have a solution available.
Finch goes to the ferry to meet his friend. Meanwhile, Hersh drives the unconscious Asif to the ferry dock and slaps him awake, after tying his hands to the steering wheel. When the terrorist wakes up, he discovers that it's his van, and the bomb is still in the back. Hersh tells him that he'll get to complete his mission after all and walks away.
Nathan spots Finch waiting for him and starts to come over, saying it's time for them to face the music. The van blows up behind them, destroying the ferry.
While Reese bandages Root's flesh wound, Finch explains that he designed The Machine so it could only accept alterations to its programming when attacked. He distributed his own virus so that whoever was responsible would use it instead, and Reese realizes that his partner hid a virus within the virus. Finch apologizes, explaining that he realized too late that he gave The Machine to the wrong people. He kept Reese out of the loop because he hoped that Reese would continue their work if Finch was killed.
The containment breach alarm shuts off and they figure that the government men are on their way. Finch wants to take Root with them because leaving her behind would mean her death. Hersh and his men come in and Reese and Sam prepare to shoot back. The Special Counsel enters and admits that he's surprised that Sam has turned traitor. She ignores his taunt and asks what he wants, and he asks Finch where he moved The Machine because the country is defenseless. Finch says that it moved itself and that no one controls it now, and the U.S. only is less defended. It will send Numbers if it wants to send Numbers. The Special Counsel gives his word that Finch can have anything he wants if he'll either get The Machine back or create a new one, but Finch reminds him that the government gave their word to Nathan, and Nathan is dead. Finch leaves with the others, and the Special Counsel asks if Sam thinks she's choosing the right said. She points out that he lied to her as well and leaves.
Finch wakes up in an emergency ward and discovers that he's covered in blood. A nurse warns him that he sustained injuries to his back and neck. As she moves off, Finch sees the doctors trying and failing to resuscitate Nathan. Two government men are standing nearby and call to inform their superior that the problem is taken care of. Finch limps toward the door but hides behind a privacy screen when Grace comes in. The medics direct her to a table with personal effects and Grace goes over and finds Finch's engagement ring, inside of the book he gave her. The government men approach Grace and Finch realizes that he can't approach her without putting her at risk. As Grace breaks into tears, Finch limps off.
Back at the library, Finch asks The Machine if he knew. As it starts erasing its information at midnight, Finch discovers that Nathan was the last non-relevant that it registered before he shut it down earlier.
The caretaker at the facility tells the Special Counsel that he received a call from the Special Counsel to move The Machine, and that they transferred it a node at a time so it would remain active throughout the process. He has no idea where the nodes were going. Control calls the Special Counsel and he tells her that they'll track down The Machine eventually. She asks to speak with Hersh and the Special Counsel hands over the phone. After listening to his superior, Hersh says that he'll seal the room. He shoots and kills the caretaker and then his own men. The Special Counsel says "fair enough" and stands calmly as Hersh guns him down.
Back in New York several days later, Reese and Finch are out walking Bear. They haven't received a Number since they went to the facility and Finch admits that he doesn't know if they ever will. He then apologizes to Reese for getting Jessica killed by distributing the virus to free The Machine. He admits that he knew someone might get hurt but didn't consider the personal cost. Reese tells him that he had already made his decision when he walked out on Jessica years ago and didn't say what he had to. As they talk, a nearby pay phone rings.
Hersh tells Control that Research has reestablished contact with them, and she tells him to form a team.
Root is being held at a psychiatric ward, wandering the floor. A nearby pay phone rings and she answers it. The Machine asks "Can you hear me?" and she says "Absolutely."