In Bishop, TX, 911 receives a call about a missing girl, Hanna Wrey.
Reese meets with Carter and Fusco for a morning drink and reminds them that Finch has been gone for 24 hours. Carter has checked the SSN that the Machine gave them on Hanna Wrey and confirmed that she disappeared in 1991 after leaving the library one night. She would be approximately the same age as Root from what little they know of her, but Carter hasn't found anything else about her. Reese refuses to tell them where he is getting his information from but figures that solving Hanna's disappearance will lead them to Root and Finch. While he goes to Bishop with Carter, Fusco will work the Corwin case and determine who is messing up the investigation, and take care of Reese's new dog, Bear.
The Special Counsel calls Hersh at the police station to check on his progress. Hersh informs him that he's shut down the investigation, and has found a key in Corwin's possessions. He glances over at Fusco, who is struggling with Bear, and assures the Special Counsel that no one should get in his way.
Reese and Carter check into a motel at Bishop. The manager tells them that they're lucky to get a room since deer season has just started and there are hunters camped out in the parking lot. Carter is less than thrilled that they got a single bed but Reese assures her that he'll sleep on the floor. They go to the sheriff's department and Carter insists on dealing with law enforcement while Reese gets a low profile. She gets nowhere with Sheriff Landry, who refuses to give her privileged information without knowing who her suspect is in what she claims is a related case in New York. Meanwhile, Reese realizes that Carter is getting nowhere, impersonates a delivery room, enters the station, and steals the files on Hanna Wrey's abduction. Carter comes out and they review the files. On the night of the disappearance, a young girl called 911 and reported a license plate number, but the police were never able to trace it. Carter figures that they need to start from the beginning and talk to the last person who saw Hanna.
In Relton, MD, Root ties up Finch and talks about how humanity is bad code and that Finch leaves in fear and anonymity as a result. She blames him for selling the Machine to the wrong people and then goes over to Weeks, who she has tied up from the ceiling, and says that either Finch or Weeks will walk out with her, and she hopes that it's Finch.
Reese and Carter talk to the librarian, Barbara, who says that in 1991 Hanna played games on the library computers. Barbara tells them that Hanna checked out two books and left by herself, and that was the last anyone saw of her. Reese and Carter go to see Mr. Frey, a widower, and he accuses Cody Grayson, a teenager at the time, of killing Hanna. Even after Frey and his brother paid Cody a private visit, he claimed that he never touched Hanna. Since then, Cody spends most of his time drinking at the Razorback bar. As they leave, Carter notices some mail on the table and asks Frey if anyone ever reached out to him about the disappearance. He explains that he gets credit card junk mail a couple of times a year in Hanna's name, even though she was minor and never had a bank account or credit card. Frey says that he just received another mailing and that it's still out in the trash.
Fusco calls Carter to tell her that some of Corwin's belongings have disappeared from inventory. Carter figures that they need to track down the person responsible and get some answers from him. Fusco notices Hersh, a newcomer and busy on his telephone, and decides to follow him. Meanwhile, Carter finds the junk mail addressed to Hanna. Meanwhile, Reese goes to the Razorback, much to the anger of the locals, and tries to talk to Cody. Cody throws a punch at him and the other bar patrons rush in, but Reese takes them out and tosses Cody out through the door. He asks if Cody did it and Cody says that there's nothing Reese can do to him that the townspeople already haven't. Reese realizes that he didn't abduct Hanna as Carter drives up. She tells him that she's confirmed that someone opened a bank account in Hanna's name two years after she disappeared.
Root informs Weeks that she's using the same Palestinian hanging technique on him that he signed off on at the DoD. She demands to know the location of the Machine but Weeks insists that he has no idea what she's talking about. Root puts the hood back on him and Finch wonders what happened to her to make her the way she is, but Root claims that nothing specific happened to her. She goes to cut an apple and give Weeks time to weaken. However, when Finch asks her to let Weeks go, she agrees and cuts him down, and then gives him water. Root then tells them that she gave him sodium pentothal in the water. She goes to bring her car up to the house and give the drug time to work. Once she leaves, Weeks realizes that Finch was Nathan's IT guy and asks for his help getting free, insisting that they can't let Root get the Machine.
Reese and Carter go back to the motel and she explains that in 1993, someone using Hanna's name opened a bank account in Lafayette, LA, and then transferred $100,000 to it. The money came from the account of a drug trafficker, Jose Barilla, who was in prison for drug trafficking and murder. The co-signatory on the account is Trent Russell, who lives in Bishop, works as a bank clerk, and was at the library on the night that Hanna disappeared.
When Carter and Reese go to Trent's home, they discover that he's been dead for 15 years and that his wife is Barbara the librarian. She explains that she met her husband at the library, and that he died when he was killed by drug runners. Barbara insists that he didn't deal in drugs and that he didn't know Hanna, and orders them to leave when Carter shows her the bank account with his signature on it. Reese and Carter refuse and search the house, and Reese discovers that Trent's car has a license plate that is only one letter off from the one reported in the 911 call. They figure that Hanna escaped, set up Trent, and got her revenge by letting the drug runners kill him. Carter insists that they let the law handle it and calls Landry in.
Finch tells Weeks that he knows he attempted to hack the Machine and Weeks admits it, saying he had to make sure it was secure. When Finch vows that Root won't find out about the Machine from him, Weeks points out that she'll eventually break him and get the info from him. He convinces Finch to help him and the programmer manages to knock a knife off a table. Weeks uses it to cut himself free and then attacks Hanna when she comes in. He mercilessly beats her until she passes out and then takes her gun. Weeks has figured out that Finch created the Machine, not Nathan, and says that he wants to know what he knows.
Landry arrives to take Barbara into custody while Reese and Carte continue searching the house. They find sixteen copies of Flowers for Algernon, the book that Hanna checked out on the day she disappeared. Barbara tells them that someone has mailed her a copy every year on the anniversary of Hanna's disappearance. There's a Seattle receipt in the most recent book and Reese goes back to the motel to check it out while Carter continues questioning Barbara.
Weeks assures Finch that he'll have his people interrogate Roots, but asks him to confirm that the Machine can't be accessed. Finch finally admits that only someone with physical access can reprogram the Machine, and Weeks tells him that the Machine is still safely hidden. The DoD agent then says that it's an honor to meet him and shoots him with the gun he took from Root. However, the gun is empty and Root tasers Weeks unconscious. As she gets up, Root tells Finch that Weeks is another example of how humanity is "bad code."
Reese goes back to the motel the next morning. Some of the locals are waiting for him but he takes them out and then steals a crossbow and a laptop from one of the hunter's trucks. He then calls the bookstore in Seattle and, posing as Stills, starts tracking down the buyer.
Carter and Landry play the 911 call for Barbara and she tells them that she already knows who made the call. It was Hanna's friend Samantha Groves, who was at the library the night that Hanna disappeared. In 1991 Sam was 12 and lived with her sick mother outside of town. The librarian admits that she knows who made the call because Sam came to her and told her that she saw Trent drive away with Hanna. Barbara, who had fallen in love with Trent and didn't believe he could do it, told her that she was lying to get attraction and browbeat her into remaining silent. Carter wonders if Barbara believes Trent did it now and the librarian tells her that two weeks after the disappearance, Trent redid the patio.
Reese traces the money from the Seattle bookstore. When the hunters come in to get their gear, Reese aims the crossbow at them and tells them to get out.
The police dig up the patio and find a corpse and a buried backpack. Inside the backpack is the copy of Flowers for Algernon that Hanna checked out.
Using his stolen police ID, Reese traces the purchase from the bookstore through a bank and to a credit card account. Someone purchased gas at a station in Relton, MD, and Reese realizes that's where he can find Root.
Finch realizes that Root set up Weeks to demonstrate her point about humanity, and she says that he gave the Machine to violent and predictable people just like Weeks. Root wants to work with him, saying she'll be the best partner he could ever have, but he tells her that it will never happen.
Carter meets Reese at the hotel and he tells her that he's tracked down Hanna. However, Carter tells him that they found Hanna's corpse beneath the patio. She's checked and learned that Sam Groves left Bishop ten years ago and they figure that she's Root.
After Hanna abandons her computer game and leaves, Hanna sits down and finishes it in a matter of seconds. She then goes to the window and sees her friend get in the car with Trent, who drives off.
Fusco follows Hersh after jacking into his phone. He listens in as Hersh calls his superior, who tells him that Weeks has disappeared. The Special Counsel tells Hersh to check on Weeks' mistress, Julie Davenport, who has a home outside of DC.
Root returns and injects Finch with a sedative so she can safely transport him. Her bank calls to tell her that someone has been tracing her credit card account and, surprised that Reese could do the work, wonders if the Machine is helping him. Root then puts Finch in a wheelchair and tells him that they're going to the train station. She then interrogates Weeks and asks where the Machine is, pointing a gun at him. Weeks finally cracks and tells her that all he knows is that it was shipped to Des Moines, put on a train, and transported to salt Lake City. He warns Root that she doesn't know what she's getting into, but she shoots him dead. Meanwhile, the semi-conscious Finch has managed to get to her cellphone and dial a number. When Root sees what he's done, she tells him that she disconnected the phones and then hauls him out... unaware that Finch has dropped his cufflink next to the discarded cellphone.
Reese goes to the gas station where Root bought gas and IDs her from the station security footage. He calls Fusco, who has already figured that Root has Weeks, and tells the detective to check for property records belonging to Julie Davenport.
At the train station, Root reminds finch that she'll hurt innocents if he struggles and then leaves him while she goes to check on the train schedules.
Fusco gets Davenport's address and sends it to Reese. Reese finds the corpse, Finch's cufflink, and the cellphone. He brings up the last number dialed and realizes that Finch tapped out letters in code. Deciphering them, he realizes that Root is taking Finch to the train station.
Root comes back and takes Finch to the train, but spots Reese as he enters the station. She pushes Finch back behind a pillar, and Finch insists that Reese disproves her theory that all humans are bad code. As she prepares to shoot a security guard, Finch manages to shove himself out so that Reese can see him. he then lunges out of the chair, ruining Root's aim and saving the security guard. As root runs off, Reese stops to confirm that Finch is okay. When Finch says that he didn't intend for Reese to save him, Reese says that he owes him for saving his life.
That night, Carter returns to the station and tells Fusco that they got Finch back. The two detectives go out for drinks.
Finch and Reese go back to the library and Finch is surprised to discover that they have a new dog... that likes to chew up first edition books. He tells Reese that he owes him for saving his life. Root calls and thanks Reese for giving her friend Hanna a proper burial. She promises that she won't forget, but Reese tells her that she'll be sorry if she comes after Finch again. Root tells him to tell Finch that she'll be coming for him when she's ready and then hangs up. She then returns to watching the DoD agents as they take Weeks' corpse away.
Sam finishes her computer game by signing the name "Root" to the high score.