After setting up the Machine on January 1, 2002, Finch has it confirm that he is the Admin. For the next 3,791 days the Machine monitors Finch and Ingram talking about the Machine, Corwin warning Ingram that what they're doing is illegal, and Finch recruiting Reese. Finally the Machine reviews the events of the last few days when Root, posing as Caroline Turing, makes sure that she picked as the next number and gets close enough to kill Corwin and abduct Finch.
Reese tells the Machine via a traffic camera that he needs its help to find Finch. A nearby phone ring and when Reese answers it, a computer voice announces three three-word combinations and then disconnects.
The Machine finally locates Finch in a diner with Root. When a police officer enters the diner, Root tells Finch that she knows that he cares about others so she will shoot someone else, not him, if he calls for help. When Finch wonders what she knows, Root says that she knows enough and doesn't believe his denials. She tells Finch that they're going to the future and that she's been looking for him her entire life. During her life she's been smart enough to do anything she wanted to and get away with it, until Finch stopped her by anticipating what she would do. Root knows about the Machine and Finch's role in creating it, and points out that it didn't protect him.
When Carter returns home, she discovers Reese waiting for her. He assures her that her son is safe with a friend and then explains that Root took Finch. However, he doesn't want Carter to file a missing persons report because he figures that Finch is off the grid for a reason. Reese wants Carter to run a check on Alicia Corwin, the woman that Root killed to get to Finch, while he chases down a lead.
Back at the library headquarters, Reese goes over the Machine's three three-word phrases. When he picks up a nearby book and notices the spine, he realizes that each three-word phrase represents a title, last name, and first name. When he puts the three books together, the Dewey Decimal numbers make a Social Security number. Reese then calls Fusco and has him traces the SSN. The detective confirms that it belongs to Leon Tao, an accountant with no criminal record. He activates the tracer on Leo's car and Reese follows the signal to a bar.
Leon is talking to a man with an Aryan Brotherhood tattoo, and Reese flashes Stills' stolen badge at him to get him to move away. He then sits down with Leon and shows him photos of Finch and Root, but Leon insists that he doesn't know them. Glancing around, Reese notices that the first man and two others with him all have guns and realizes that the Machine sent him there to protect Leon, not to find Finch. The first Aryan comes over and tells Reese that Leon stole money for him. Reese isn't interested and says that he just wants to leave peacefully. When the Aryans decline, Reese quickly takes them out and leaves. Leon has no choice but to follow.
2002 - Day 47
Finch tests the Machine's capabilities by going out on the street and then trying to avoid its electronic surveillance. He goes into a diner with no cameras, but the Machine contacts him via his cell phone and a pleased Finch realizes that it's watching him on a laptop webcam.
Leon is puzzled when Reese stops to talk to a camera, telling the Machine that he knows that he's Finch's contingency in case the programmer disappeared. The accountant starts to leave only to discover that they've towed his car. He asks Reese for help, insisting that he was negotiating with the Aryans, but Reese doesn't believe it and Leon admits that he stole $8 million from them. Leon lost his job and went to work for a startup company, only to discover that the Aryans were using it as a front to launder their drug profits. He stole their money and left but they tracked him down. Reese breaks the window on a police car, setting off the alarm, and then handcuffs Leon to the door handle. As he walks away, Reese calls Fusco and tells him that Leon will be coming in and to keep an eye on him. Fusco is less than thrilled at the grunt work, especially when he looks over at Carter and sees her working on Reese's investigation into Corwin.
Deputy Director Denton L. Weeks meets with his superior, the Special Council, who informs him that his agent Alicia Corwin is dead. The Special Council warns that her death threatens their project and calls in his NYPD contact, Hersh. Hersh assures them that he will make sure that the investigation on Corwin's murder dead-ends. The Special Council tells Weeks that his group will handle security from now on and then shows him a photo of Reese from his recent attack on their men defending Peck. Weeks doesn't recognize him and wonders who he is, and Hersh promises to ask before he kills him.
After going over the info that Finch gathered on Root, Reese calls Carter and tells her that the Caroline Turing driver's license she used is legitimate. He figures that she has a contact in the DMV and has Carter check on who could have issued it off the books. As Carter talks, Fusco overhears her and complains that she's on a first-name basis with Reese. Meanwhile, Leon fakes a heart attack and escapes from holding. When Fusco gets word, he calls Reese, who tells him that Leon is heading to the impound lot to recover his car.
Fusco catches up to Leon and the accountant warns that the Aryan Brotherhood will kill him once he's in jail. Before they can leave, Byron and two of his Aryans how up with guns and demand the $8 million that Leon stole. When he refuses, they prepare to kill him and Fusco suggests that Leon's life is more important than the money. Leon reluctantly gets $1 million in bearer bonds out of his car and claims that he lost the rest when the market tanked. Fusco draws his gun and tells the Aryans to let them go, but two more Aryans ambush him from behind.
2003 - Day 614
Finch goes to a casino and has the Machine monitor him via the security cameras while he plays blackjack. Thanks to its messages via his cell phone, Finch soon wins big and an older man congratulates him. However, Finch soon has second thoughts, ignores the Machine's advice, and loses everything. The older man consoles him as Finch looks up at the camera and smiles.
Root takes Finch to a pharmacy to buy some supplies for their trips. When he argues with her, Root cuts his hand and warns him that from now on, she'll hurt him. The pharmacist comes over to tend Finch's injury and Root uses the distraction to slip behind the counter and steal some pills.
Reese goes to the apartment of the DMV employee, Owen Reynolds, and discovers that he's been gone for days. Carter calls to tell him that Fusco has gone missing.
Byron takes Fusco and Leon to the Brotherhood headquarters and threatens to sic his dog Butcher on them. Leon still insists that the $7 million is gone and Byron gets out a pair of bolt cutters. Two of the Aryans find Reese outside and bring him in. He says that he's just looking for his friends and suggests that Byron let them go. When the Aryan refuses and threatens him with the dog, Reese, explains that he and his men used the same breed in the service and that there are only three Dutch trainers who handle them. Byron sics the dog on him but Reese tells it to heel in Dutch and then tosses the Aryans out the windows. As he leaves with Fusco and Leon, Reese whistles for Butcher to come with him.
2003 - Day 615
As Finch leaves the casino, the Machine calls him on his cell phone and sends a single text message: Stay. Finch ignores it and starts to walk across the street. The Machine sends the same message and Finch looks at it, stopping jut as the old man from the casino passes out and drives his car by, narrowly missing the programmer and hitting a fire hydrant down the road. Back at his office, Finch tells the Machine that its job is to protect everyone, not just him, and says they have to lay down some ground rules.
Root takes Finch to another restaurant and she grinds up the pills she stole while she explains that when she was a child, she understood computers better than people. She then points out a blonde woman at the next table and explains that she may look normal but actually she lies on her taxes, is addicted to painkillers, and sleeps with a married man. Root then drops her lipstick and the blonde woman picks it up, unaware that Root has slipped the ground-up pill into her drink. Back at the table, Root tells Finch that her victim will be fine... in a couple of months. She dismisses people as bad code but says that Finch's Machine is perfection. He tells her that it's just a machine but Root knows that if he created a machine capable of predicting human behavior, he must have given it sentience. However, she complains that once he did create the perfect Machine, he gave it to corruptible government employees. The woman at the next table collapses from the drugs and Root steals her phone in the confusion and escorts Finch out.
That night, Reese drives Leon to the airport so the accountant can skip town. As he pets his new dog, Carter calls to tell him that she went to Reynolds' apartment, checked his mail, and found an unpaid bill for a storage unit. Reese tells Leon that they're taking a detour and drives to the storage unit.
Titus goes to the Aryan Brotherhood headquarters and finds Byron and the others recovering from their wounds. He tells Byron to find Reese and Leon and get rid of them for good.
At the storage unit, Leon refuses to get out of the car so Reese hauls him out, tosses the bonds in the car, and leaves Butcher to guard them. Inside they find Reynolds, dead at his computer. Reese figures that Root killed the man to cover her tracks and orders Leon to check the records and figure out how she paid the DMV worker. As Leon hacks the computer, he explains that he invested the other $7 million in stocks that tanked. He then tells Reese that Root transferred the money from Reynolds from his own account.
As the two men leave the storage unit, Carter calls Reese to tell him that all of the computer records on Corwin have been "accidentally" erased and the evidence is gone. As they talk, two Aryans find the men and open fire. Reese drags Leon into an alleyway and hides until the Aryans ride by, and then goes to another traffic camera. He tells the Machine that he's not going anywhere until it helps him find Finch, and that it will have to bend its rules or it will have no one to act on its information. A nearby phone rings as the Aryans double back and Reese answers it. The Machine gives him another coded Social Security number and Reese leaves with Leon.
The Special Council calls Weeks from his Washington office and tells him that the NYPD investigation into Corwin's death is closed. When Weeks says that he's going away for awhile and will be out of contact, the Special Council ominously tells him that they can always contact him.
Reese and Leon take refuge in a parking garage as the rest of the Aryans arrive. Leon heads for the roof while Reese tries to slow their attackers down, but Titus catches Leon on the roof and demands his money. Leon insists that he doesn't have it and Reese arrives to fight the huge Aryan. Titus is too much for Reese but Carter and Fusco arrive to take out the Aryan with a beanbag slug. Leon goes to the car but discovers that the dog has eaten the bearer bonds. When Reese hears him complain, he decides to name the dog "Bear." He then tells Leon to get out and appreciate the fact that he's poor, and Leon admits that he's only 80% certain that he lost the money. As Reese leaves with his new dog, Leon tells him that Finch is lucky to have him as a friend.
Back at the library, Reese translates the new SSN and discovers that it belongs to a 14-year old girl, Hanna Wrey, who disappeared in Bishop, TX, over a decade ago. He goes to meet Carter and tells her that she's going on a road trip with her to Texas to find out where Root came from.
Root takes Finch to a quiet home in the suburbs and tells him that their friend will be there shortly. He warns Root that she can't access the Machine but she promises him that she's always able to find the flaw in something. She explains that since humans have gone as far as they can, bad code and all, she wants to see what happens next. Finch tells her that the two of them are alike and that he wanted to fix people. However, he sealed the Machine to protect it from just those type of people. When Finch warns her that he'll never help her get control of the Machine, Root tells him that he won't have to. Denton Weeks comes in and Root knocks him out with a syringe and tells Finch that she plans to set the Machine free.