The Machine reviews the events leading up to Carter's death.
Finch is out walking Bear when Sam calls him to ask if they have a new Number. She's bored and wants something to do, and warns that she doesn't do quiet well. Finch admits that The Machine hasn't called him since Carter's death, and Sam asks if he's heard from Reese. Her employer notes that Reese disappeared from the hospital as soon as he could walk out, and he hasn't heard from him since. A nearby payphone rings and Finch ignores it, and all of the nearby payphones start ringing as well.
In Colorado, Reese hitches a ride into a small town and goes to the local bar. He looks at the photos of Vietnam-era soldiers mounted behind the bar and then orders a whiskey. When a biker picks a fight behind him, Reese ignores it.
At the library, Finch visits Root and she asks him for a specific book on false gods. Once he gives it to her, Root says that she knows that he's had a rough time since he lost Reese, but says that Finch shouldn't take it out on The Machine. She somehow knows that "she" has a new Number for Finch and reminds him that The Machine wants them working together. Finch ignores her and leaves, and Sam arrives and asks if they have another Number. He says that he hasn't decided, surprising her, but finally looks it up. He discovers that the new Number is Arthur Claypool, and Finch stares at the man's photo in seeming recognition before telling Sam that it's time to go to work.
Finch tracks down Arthur to a hospital where he used his credit card and Sam goes in posing as a doctor. As she looks for Arthur, Finch tells her that Arthur recently worked as an IT consultant with a software company in Maryland. There's no record of Arthur in the hospital computer system, but Sam spots him in the cancer treatment lounge. Finch confirms that Arthur has a terminal brain tumor, and Sam approaches him. He doesn't recognize her but admits that he's having memory problems because of the tumor. Arthur has trouble recalling some memories but blurts out others at random. As they talk, Arthur suddenly starts blurting out instructions to someone about checking the database.
A man, Easton, comes over and asks who Sam is. She shows him her fake ID and quickly leaves. She then tells Finch that Easton is a government man and watching over Arthur, and they figure that Arthur supposed job is a cover story and he does top-secret work for the government. Easton and two other men escort Arthur away in what Sam recognizes as a classic three-man wedge formation, and Sam realizes that they work for the Secret Service.
In 1969, a young Harold Finch is watching birds at his family farm as his father works on a flooded truck engine. When Harold asks about the birds, his father offers to help him identify them if Harold helps him with the truck. Harold agrees and notices that his father has forgotten where he put his wench. He gives it to Mr. Finch and they work on the engine, and Harold's father talks about how every piece has a reason for being there. The phone rings in the house and Mr. Finch goes to answer it. When he comes back, he discovers that Harold has taken apart the engine and neatly arranged all of the pieces on the work bench. When Mr. Finch warns his son that he shouldn't be taking things apart, Harold says that if they don't want someone to do it then they should build a better engine.
Sam is unable to get close to Arthur again because of Easton and his men. Finch checks and discovers that Arthur has a non-existent digital footprint, confirming that he has a top-secret clearance. Sam suggests that he come and create a distraction since Reese is gone, but Finch says that he needs to stay with Root, who is acting unruly. Sam spots a woman with flowers coming to see Arthur, and Finch verifies that Arthur has a wife, Diane. When Diane goes inside, Arthur yells at her and Sam tries to go in, but Easton and his men stops her. Arthur is yelling that he doesn't remember Diane and that he has to fix Samaritan, and that he won't let "them" kill it. Easton tries to shush him up, while Sam tells Finch what is going on. He informs her that the name "Samaritan" sounds familiar.
When the Secret Service men won't let her through, Sam visits with Diane in the lounge. She insists that Arthur is harmless but admits that her husband works for the NSA. Diane talks about how she keeps coming back in the hopes that her husband will remember her but that it's hard on her after all of the years together. Sam goes back to check on Arthur and discovers that Easton and his men have taken him to Radiology. As she goes after them, Finch informs that he's done some digging and confirmed that Samaritan is a classified NSA project that Congress shut down in 2005. Sam figures that any number of foreign intelligence agencies are after the information that Arthur is freely telling anyone and everyone, and Finch figures that Easton may be there to kill Arthur if he becomes a security risk.
Sam slips into the room via the ceiling and finds a discarded syringe in a wastebasket. Confirming that it contained sodium pentothal, Sam listens as the technician questions Arthur. He says that Rudy has them, and the technician leaves as Sam steps out. Easton and his men burst in and capture Sam.
In 1971, Harold has built a homemade computer memory system in the kitchen. He tells his father that he designed it so that it would remember things for him, but Mr. Finch warns that no one can fix what's wrong with him. Harold insists that he can build a machine containing all of his father's memories, a machine that can think. Touched, Mr. Finch still tells him that not everything that is broken can be fixed, and asks his son if he understands.
Easton and his men lock Sam up in an empty office. While she waits, Finch calls her on a cell phone left in the drawer and tells her that he's in the parking lot. Sam tells him to watch Arthur but Finch refuses. However, he checks the hospital cameras and confirms that the technician signed in using the name "Elizabeth Ross." Easton comes in and Sam hastily hides the phone, and the Secret Service agent asks why she's interested in Arthur.
In Colorado, Reese notices Fusco sitting at a nearby booth and goes over to confront him. Fusco admits that he tracked Reese down with some help from Finch, and Reese tells him to go home. The detective refuses and joins him at the bar, and Reese tells him that he'll have to drink and be quiet if he's going to stay there.
As Easton eats some Chinese takeout, he questions Sam, who realizes that he hasn't done any field work. She advises him to focus on Arthur and warns that the people who tried to interrogate him will come after him again. Easton collapses, unconscious, and Sam realizes that someone drugged his food. She calls Finch, who admits that he isn't responsible for the drug, and notes that "Elizabeth Ross" is the full name of Betsy Ross of Revolutionary War fame, meaning the technician is working for Vigilance. As they talk, Finch spots Collier and a hit squad pull up outside and warns Sam.
Sam checks on Easton's men and discovers that they've also been drugged unconscious. She goes to Arthur's room and Diane wonders why she has a gun, but Sam simply says that they have to go. Arthur refuses to go, since he can't remember either of them. However, Finch comes in and addresses him by name. Arthur recognizes him and says that he's glad that he's there, and Finch says that it's been awhile.
1979 in Lassiter, Iowa, and a teenaged Howard is hanging out with two of his buddies. They talk about what is going on outside of Lassiter and Howard offers to let them talk to someone in Paris. He goes to a payphone and uses a whistle to hack the system, making a free call. As he and his friends share a laugh, a state trooper pulls up. He has Mr. Finch in the back seat and tells Howard that it's about his dad.
As Finch leads Arthur out of the hospital, Arthur talks about how they studied at MIT together and knew that Finch would be the one among them who would change the world. A Visionary agent draws a gun on them and Sam kneecaps him, and they escape in Finch's car. Finch drives to a hotel and explains that the anti-surveillance Visionary organization is after Arthur because he worked for the NSA. Arthur doesn't remember anything about Rudy and wonders why Finch is involved, but Finch dodges the question. Diane wonders who they are and Sam simply warns her that they can't trust the Secret Service.
That night, Sam stands watch while Arthur and Finch talk about their time together at MIT. Finch finally turns the conversation to Samaritan and his friend explains that it's an AI designed to anticipate and stop terrorist attacks. The system learns from experience and upgrades itself. Sam overhearing, talks with Finch privately and they realize that Arthur built a second Machine.
The state trooper drops Howard and his father at home, and explains to Howard that Mr. Finch was out wandering the roads after dark in near-freezing weather. He advises Harold to put his father somewhere where he won't hurt himself and where he can be taken care of. Once the trooper leaves, Mr. Finch tells his son that he's wasting his life taking care of him. Harold insists that he'll stay in Lassiter and if he can't go to the information then he'll bring it there. His father tells him not to be reckless but Harold echoes their conversation from years ago, saying that if they don't want people to get in then they should build it better.
Finch asks Arthur what happened to Samaritan and the man says that it was destroyed in 2005, just a few weeks before Arthur insists that he would have finished it. After 9/11, the NSA hired numerous contractors to create an anti-terrorist surveillance system, but then shut down everything in 2005. Arthur is convinced they did it because they created a working AI system and shut down the other projects to throw people off the trail.
In Colorado, Reese notices that Fusco is drinking club soda. The detective explains that he's been two years sober, ever since Reese found him and showed him what he was. Fusco then asks Reese why hiding out in his father's bar will solve anything. Reese explains that his father owned the bar before he served in Vietnam, but he died in a refinery accident two months after he came back from his last tour of duty. Looking around, Reese figures that nothing matters because bad things happen no matter what they do to stop them. Disgusted, Fusco tells Reese to go outside with him. Once they are, Fusco punches him and finally provokes Reese into fighting back. The two men tackle each other just as a police car pulls up.
Finch uses his laptop to create new IDs for Arthur and Diane and sets them up at a hospital in Toronto where his friend can get treatment. Arthur panics, wondering why he can remember Finch but not Diane, and finally tells Finch that he buried Diane two years ago. Diane whispers into a wrist radio, saying that it's a go, and her men burst into the hotel room. They subdue Sam and Hersh comes in, and Diane explains that she's Control, Sam's former employer. She thanks Sam for saving Arthur's life at the hospital and leading them to Finch.
Control draws a gun and tells Arthur to give them the drives containing the Samaritan project. Finch speaks up, insisting that his friend doesn't know. Control tells Finch that he has something of hers as well and he's going to return it to her. When Finch refuses, Control tells him that the man who tells her what to know will be the one who gets to leave.
The Machine, listening in, registers the existence of Samaritan and begins tracking the increasing chance that it will conflict with The Machine.