January 1, 2002 – Day 1
Finch sets up the Machine to scan him and confirm that he's Admin.
Finch reminds his partner Ingram that they built the Machine to spot terrorists before they could act.
Agent Corwin warns Ingram that he'll go to jail if Congress finds out what he's doing.
Finch tells Reese that he wants him to act on the knowledge he gathers.
Finch admits that both he and Reese will probably end up dead.
The Machine provides a new number for Caroline Turing.
While Reese realizes that Root posed as Caroline to lure them out, Root captures Harold. Reese then turns to the Machine, talks to it via a camera, and tells it that it's going to help him get Harold back.
A nearby phone rings and Reese answers it. A computer synthesized voice states several seemingly random words and then cuts off. Meanwhile, the Machine keeps searching for Harold and finally finds him a diner with Root. A police officer sits nearby and Root warns Finch that if he calls out, he'll shoot someone else. She asks him not to make him do it and he nods but refuses to talk. Root tells him that she knows enough and Harold asks where they're going. She tells him the future and when he denies he's who she's looking for, Root says that she's been looking for him her entire life. When Finch points out that she's a murderer and a thief, Root points out that he's the only one who stopped her by knowing what she was going to do. She knows about the Machine and realizes that Finch created it. She wonders why it didn't protect him.
Carter comes home and finds Reese waiting for her. He tells her that her son is studying with a friend and that Root took Finch. He refuses to tell Carter what Finch has that Root wants, and she offers to file a missing persons report. However, Reese tells her that Finch has a reason for going off the grid. While he chases down a lead, he wants Carter to investigate Root's last victim, Corwin. When she asks what he's going to be doing, Reese admits that he isn't quite sure.
Back at the library, Reese writes down the words that the Machine gave him and tries to work out what they mean. When he picks up a book and realizes that each tag has the title and initials, he looks for books that match the single word title and the two names, first and last. The Dewey Decimal numbers when placed in sequence form a Social Security number.
Reese calls Fusco and has him trace the number. It belongs to Leon Tao, a man with no criminal record. Fusco activates the tracker on Leon's car and Reese tracks him to a bar. Leon is meeting with a man who assumes that Reese is a detective. The man moves away and Reese shows Leon photos of Finch and Root. Leon insists that he's never seen either one of them before and Reese realizes that he's telling the truth. He wonders why he's there and notices that several men in the bar are carrying guns. Reese realizes that the Machine has sent him to help save Leon and that Finch set him up as the backup. Leon insists that he hasn't done anything to anger them, but the first man comes over and explains that Leon stole money from them. Reese says that he doesn't have time for it and says that he just wants to leave with Leon. They tell Reese that he should just leave and Reese goes after them while Leon ducks beneath the table. Reese disposes of them and asks Leon if he's leaving with him, and the man quickly goes with him.
Day 47 - 2002
Finch goes out on the street and talks to the Machine via a surveillance camera. It signals him via his cell phone and he tells it that they're going to play hide and seek. The Machine continues to track him using laptop webcams, much to Finch's satisfaction.
As they walk down the street, Reese addresses a camera, telling the Machine that he knows Finch programmed it to keep giving him numbers. Leon has no idea what he's talking about and starts to walk away, only to discover that they're towing his car. He asks Reese to help get his car back, explaining that he was just negotiating with the men at the bar. Reese has identified them as Aryan Brotherhood from their tattoos and points out that they had guns. Leon admits he stole $8 million but he didn't intend to. He took a job at a startup company and discovered they were using it to launder profits from their meth operation, so decided to do take some payback. Reese breaks into a police car, takes the handcuffs, and handcuffs Leon to the door. After leaving him for the police and walking away, Reese calls Fusco and tells him to make sure that Leon doesn't get hurt while he's in jail. Meanwhile, Carter starts an investigation into Corwin's death.
Deputy Director Denton L. Weeks meets with the Special Council, who informs Weeks that Corwin is dead and it threatens their project. He calls in his NYPD contact, Hersh, and tells him to make sure that the investigation goes elsewhere and informs Weeks that his group will handle security. As Weeks goes, the Special Council shows him a photo of Reese and explains that he was protecting an analyst, Peck, who had contact with Corwin. When Weeks wonders who he is, Hersh tells him that he'll ask just before he kills him.
Back at the library, Reese goes over the information he has on Root and then calls Carter. He tells her that her driving license was real and has Carter call the DMV and find out who issued it off the books. She agrees as Fusco overhears her. He calls to check on Leon and discovers that he managed to slip out of holding. Fusco reports to Reese, who tells him where Leon is going and warns him not to lose Leon again.
Leon goes to the impound lot and recovers his car, but Fusco catches up to him and says that he's taking him back to jail. The accountant insists that the Brotherhood will kill him in prison. Three Brotherhood members show up and draw guns on him, and Leon refuses to give over the money at first. Fusco convinces him otherwise and Leon gets their money from the trunk of his car. There's only a million and Leon claims that there's nothing left. Fusco draws on them and insists that Leon is going with them, but two more men come up and knock Fusco out from behind.
Day 614 - 2003
Finch goes to a casino and plays blackjack. The Machine hacks into the casino security cameras, identifies the cards through the backs, and sends him advice on hitting on his cell phone. It's wrong the first time but soon learns the optimal strategies. Finch is soon winning big but has second thoughts and ignores the Machine's advice, hitting instead of staying. He looks up at the camera and smiles as the Machine registers a user error.
Root takes Finch to a store to buy a few things for the trip. She cuts his hand and assures him that he'll be the one she hurts. As the pharmacist tends to Finch's injury, Root steals some drugs from behind the counter.
Carter checks with Reese, who has confirmed that the DMV employee who sold Root the driver's license has disappeared. She tells Reese that Fusco has gone missing.
The Brotherhood man, Byron, takes Fusco and Leon to their headquarters and informs the accountant that Titus will soon be there. Leon insists that the money is gone and Byron takes out a pair of bolt cutters. Two of Byron's men bring in Reese after finding him lurking around outside. He suggests that Byron just let them all go, but Byron tells him it's not going to happen. As Byron's guard dog Butcher barks, Reese explains that trained dogs bark from anxiety and it doesn't like Byron. Byron slaps him but Reese continues, explaining that they used similar dogs in the service, and the same three Dutch trainers provide the dogs. Byron releases the dog but Reese orders it to sit quietly. A few seconds later, Byron goes out the window. Reese leaves with Fusco and Leon and whistles for the dog to come with him.
Day 615 - 2003
Finch leaves the casino and the Machine calls him. It tells him to stay but Finch ignores him. The Machine sends him the stay message and Finch starts to cross the street... just as a man from the casino drives past him and slams into the curb. He goes back to his office and tells the Machine that its job is to protect everyone, not him.
Root takes Finch to another restaurant on the beach and admits that she doesn't like killing people but she doesn't mind it, either. She grinds up some of the pills she stole and tells Finch that computers make more sense to her than people. Root talks about the woman at the next table and how she looks normal but lies on her taxes, is addicted to painkillers, and sleeps with a married man. She then drops her lipstick next to the woman and drugs her drink when she gets the lipstick. Root assures Finch that the woman will be fine in a month or two, and she realized long ago that people are just bad code. However, the Machine is perfect. When Finch insists that it's just a machine, Root says that she knows better and that to build a machine that can anticipate human action, he must have given it sentience but then turned it over to a corrupt government. The woman at the next table collapses and Root sends a text message to someone to meet her at their place and then tells Finch that they're going.
That night, Reese drives Leon to the airport so he can skip the country, and fawns over Butcher. Carter calls to tell Reese that she got the DMV employer's mail and found an overdue bill for a storage unit. Reese changes directions and heads for the storage unit.
Titus arrives at the Brotherhood hideout and tells Byron to find Leon and Reese and kill them both.
When Reese gets to the storage unit, he tells Leon that he's going to wait to go to the airport because he's tracking the only lead he has on his friend. When Leon refuses to get out, Reese hauls him out, tosses the bonds in the car, and assures Leon that Butcher will kill anyone who approaches them... including Leon. They go to the storage unit and find the employee Owen Reynolds, inside, dead from a gunshot wound to the head. Reese figures that Root covered the man to cover her tracks but realizes that she had to pay him upfront. He tells Leon to sit down at the dead man's computer and trace the money. As Leon works, Reese asks what happened to the other $7 million. He claims that he invested it in stocks and they tanked. Leon then finds that Root transferred the money to Reynolds from his account, creating an untraceable loop.
As Reese and Leon leave, Carter calls Reese to tell him that Corwin's data file has been corrupted and the ballistics report is missing. Two Brotherhood members find them and open fire and Reese drags Leon into an alleyway. The Aryans drive by, missing them, and Reese tells a surveillance camera that he's not going anywhere until he gets a way to find Finch. When Leon wonders what he's doing, Reese glances at a nearby phone and says that he's negotiating. He tells the Machine that it may have rules, but it isn't accounting for the fact that if they're all dead then there's no one for it to call. Leon panics and offers to give up all the money, and spots the two Aryans riding down the street. Finally the phone rings and Reese answers it. The Machine gives him more words and he thanks it and then gets Leon away.
In Washington, the Special Council calls Weeks and tells him that Hersh is making the Corwin investigation go away. He tells Weeks to look out for himself because one of them is already dead, and Weeks says that he'll be out of touch for a while on a personal situation. The Special Council informs him that they can always get in touch with him.
As Titus and his men close in, Reese takes Leon into a parking garage. He sends Leon up to the roof while he grabs a car fire extinguisher and knocks out one of the Aryan motorcyclists. However, Titus catches up to Leon as he gets to Reese's car. As Butcher barks, Titus demands the money and Leon says he doesn't have it. As the Aryan prepares to kill him, Reese shows up and takes on the much bigger man. Titus takes him down but Carter and Fusco arrive and Carter knocks Titus out with a slug. Leon discovers that Butcher has chewed up his bearer bonds and Reese decides to rename the dog Bear. He points out that Leon is broke but alive, and Leon admits that he's 80% certain he lost the money. As Reese walks away with Bear, Leon wishes him luck finding Finch and figures that Finch is lucky to have him.
Back at the library, Reese goes over the new set of words and discovers they refer to a 14-year-old girl, Hanna Frey, who disappeared in Bishop, TX, years ago.
Carter comes home and finds Reese and Bear waiting for her. He says that he has a lead on Finch and tells her that they're going to Texas to check on where Root came from.
Root tells Finch that their friend will be there shortly and then they can eat. He tells her that he has no way to access the Machine but Root assures him that she can always find the flaw. When he wonders why she wants the Machine, Root tells him that human beings have come as far as they can and she wants to see what happens next. Finch admits that the two of them are alike, and he considered how to fix people. That was why he sealed up the Machine, to protect it from people like the two of them. Finch promises her that he'll never help her get control of the Machine, and Root tells him that he won't have to. Her friend, Denton, arrives, and Root drugs him and tells Finch that she just wants to set the Machine free.