A girl calls 911 about Hanna, the girl who has gone missing.
Twenty-four hours after Finch has been abducted, Reese calls Carter and Fusco and invites them for drinks... at 8 a.m. in the morning. Carter has checked on the SSN that the Machine gave Reese and learned that Hanna Wrey disappeared in 1991 in Bishop TX after leaving the library. She'd be 35, the same age as Root, and Carter hasn't turned up anything else. When Carter wants to know where he's getting his info, Reese says that he can't tell her but figures that finding Hanna will lead them to Finch. He tells Fusco to work the Corwin case and find out why she was in New York and who is messing with the investigation. Reese also tells Lionel to watch over the new dog, Bear.
The Special Council calls Hersh at the station and his man assures his boss that the investigation is shut down. Hersh also has a key from Corwin's personal belongings and figures that he can track her down. He checks on Fusco, who is busy trying to learn Dutch to speak to Bear, and Hersh assures the Special Council that they have nothing to worry about.
Reese and Carter fly into Texas and check into a motel at Bishop. Hunters are out since deer season just started and the manager takes them to the single king room. He tells them that it's the only room left and Reese assures him that it won't be a problem. Reese wants to leave for the police station but Carter says that he'll keep a low profile while she handles law enforcement. At the station, Reese waits in the car and listens in as Carter talks to Sheriff Landry. She claims she has a missing person case in New York but can't share the name, and Landry refuses to cooperate without it.
Outside, Reese notices a delivery truck pull up outside and intercepts the driver. He takes a package in and asks to use the restroom. Landry refuses to cooperate without the name of Carter's superior and she goes back out to the car. She discovers that Reese stole the file, which mentions a 911 call and a report on a license plate that didn't check out. Carter figures they need to start from the beginning and talk to the last person who saw Hanna last, and Reese suspects that Hanna became Root.
In Relton, Maryland, Root tells a tied-up Finch that humanity has become rotten and that she has brought him there to show him the bad code. She points out that even though he created an artificial intelligence, he lives in anonymity and fear, and blames him for selling the Machine to the wrong people. Root then reveals Weeks, tied up, and explains that either Finch or Weeks will walk out of there with her.
Reese and Carter talk to the librarian, who says Hanna was usually on the computers and played the games. The librarian, Barbara, says that she gave a list of everyone there that night to the police. Hanna checked out a couple of books and left alone. That was the last that anyone saw her. Reese and Carter confirm that Hanna's mother died a few years ago and go to see Mr. Frey. He figures that a fellow student, Cody Grayson, killed Hanna. Mr. Frey and his brother interrogated Cody a few weeks later but he claimed that Hanna ran away to get away from her abusive father. Now Cody spends most of his time getting drunk at a local bar, the Razorback. As they leave, Carter asks if Mr. Frey has ever heard from his daughter and he says that she gets credit card junk mail a couple of times a year even though she never had a credit card or bank account. Mr. Frey tells Carter that she can find the most recent ones in the trash.
As Carter goes through the garbage, Fusco calls to tell her that there are discrepancies between what was listed as her personal belongings and what was there. Carter figure that if they can find out who tampered with the reports then they'll get some answers. Fusco notices Hersh walking by and hangs up. Meanwhile, Carter finds the junk mail that Mr. Frey mentioned.
Reese goes to the Razorback and finds Cody at the end of the bar. He asks him about Hanna and Cody tries to punch him, and Reese easily pins him down. The other patrons come at Reese and he takes them down, throws Cody out through a glass door, and demands answers. Cody says that there's nothing Reese can do to him that the town hasn't already done, and admits that he didn't do it. Carter pulls up and tells Reese that she ran a credit check and discovered that someone opened a bank account in Hanna's name two years after she disappeared.
Root keeps Weeks tied up using the same Palestinian hanging technique that he authorized for the DoD. Finch tells her to make it stop and Weeks claims that he has no idea what she's talking about. She demands to know where the Machine is and pus the hood back on when he refuses to talk. Finch asks what happened to her and Root says that it's sweet that he thinks something caused her to be what she is.
Later, Root cuts up an apple and Finch asks her to please let Weeks down. She releases Weeks and he collapses to the ground. Root gives him water and ties him to a post, and then tells him that he just drank sodium pentothal. She goes to get her car, assuring Weeks that by the time that she gets back he'll spill everything. Once they're alone, Weeks asks Finch to help him get free, recognizing him as Nathan's IT guy and insisting that Root cannot gain access to the Machine.
Back at the motel, Carter tracks the bank account to Lafayette. Someone put $100,000 into the account in 1993 and Hanna withdrew it as cash over the next few weeks. It came from Jose Barilla, serving 17 life sentences for drug trafficking and murder. Hanna withdrew it from his account after hacking the computers. The co-signatory on the account is Trent Russell, who lives in Bishop and was in the library the night that Hanna disappeared.
Reese and Carter go to Trent's house and discover that Barbara lives there. She explains that she's Trent's widow and that he died 15 years ago. Barbara invites them in and explains that they met at the library and he was a member of the book club. He was shot by drug traffickers and Barbara insists that he had nothing to do with them. She also tells them that Trent knew nothing about Hanna. Carter shows her the bank account statement and Barbara asks them to leave. They ignore her and search the house and garage. The license plates on the car is one digit off from the one reported on the 911 call. They figure that Trent abducted Hanna and she escaped, and then faked his name on the bank account to set him up with the drug traffickers to get her revenge. Carter says that they have to handle it the right way and call in Landry.
Finch tells Weeks that he knows he tried to hack the Machine and assures him that Root won't get to the Machine through him. Weeks points out that Root will get it from him and tells Finch to push a nearby knife to him. Finch manages to tilt the table onto the floor, dropping the knife onto the floor near Weeks. He gets it and starts to cut himself loose while Hanna returns with the car and comes inside. Weeks jumps her and beats her unconscious until Finch tells him to stop. The agent figures that Finch was the one responsible for the Machine and tells Finch that he wants to know what he knows.
After calling in Landry to arrest Barbara, Reese and Carter search Barbara's house. They find sixteen hidden copies of Flowers for Algernon
, the book that Hanna checked out the night that she disappeared. Barbara says that someone mails a book every year on the date that Hanna disappeared. Reese finds a Seattle receipt in the most recent book and tells Carter to stay there while he checks it out.
Weeks tells Finch that he's going to bring in experts to interrogate Root. He tells Finch that he'll let him know but first asks if it can be accessed. Finch finally tells him that no one can alter the programming without physically accessing the hidden Machine. Satisfied, Weeks tells him that it's been an honor to meet him, points Root's gun at him, and shoots. However, the gun is unloaded and Root tasers Weeks unconscious. Once he goes down, Root tells Harold that Weeks is bad code.
When Reese goes back to the motel the next morning, he finds some of the locals waiting for him to stage a rematch. Reese knocks them out and takes a laptop and a crossbow from a hunter's truck. He then calls the bookstore in Seattle and starts tracing the buyer.
Carter and Landry play back the 911 call for Barbara and they realize that she knows who it was. Barbara identifies it as Hanna's friend Samantha Groves, who was at the library the night that Hanna disappeared. Sam was 12 and lived outside of town with her mother, who was sick. When they wonder how Barbara is sure, Barbara admits that Sam told her the same thing that she reported to 911. She also saw Trent in the car and Barbara convinced her that she was a brat lying to get attention and told her to keep her mouth shut. Barbara did it because she was in love with Trent and couldn't believe he did it. Carter asks what she believes now and Barbara looks out at the patio. She tells Carter that Trent redid it two weeks after Hanna disappeared.
Reese calls the bank that transferred money to the Seattle bookstore. The hunters come in and ask for their stuff, and Reese tells them to get lost.
The police dig up the patio and find a buried backpack. The book that Hanna checked out is inside.
Reese confirms that the credit card used to buy the book was just used to buy gas in Relton, Maryland, and figures that's where Root can be found.
Finch realizes that Root planned the whole thing, and she points out that he gave the Machine to violent and predictable people. She insists that she's the best partner that Finch will have but he says that he will never cooperate with her.
When Carter comes back to the motel, Reese tells her that he has to go and explains that he knows where Hanna is. However, Carter tells him that Hanna was the one who is buried beneath the patio. She shows Reese a photo of Sam Groves and explains that Sam's mother died ten years ago. She left town and they figure that Sam is Root.
Sam sits down and finishes Hanna's game in a matter of seconds. She then goes to the window and sees Trent drive off with Hanna.
Fusco follows Hersh and jacks his phone. Hersh calls the Special Council, who tells him that Weeks disappeared and often went to the home of his mistress, Julie Davenport, who lived outside of D.C.
Root returns and gives Finch a sedative. She gets a call from the bank confirming that Reese is tracing her purchase and wonders if the Machine is helping him. Root then gets out a wheelchair and tells Finch that they'll be taking a train trip. She then asks Weeks where the Machine is, unaware that the drugged Finch is dialing a number on her cell phone. When Root threatens to shoot him, Weeks tells her that it was transferred on a train bound for Salt Lake City and warns her that she has no idea who she is dealing with. Root shoots him dead, goes to Finch, and tells him that she disconnected the phone. However, she doesn't notice that Finch has dropped one of his cuff links on the carpet.
Reese goes to the gas station and identifies Root on the security footage. He calls Fusco, who says that Root probably has Weeks as well. He checks the property records for the mistress while Reese takes off.
At the train station, Root parks Finch and reminds him that if he tries anything, people will get hurt. She goes to check to see if their train is on time.
Once Fusco has the address, Reese goes to the house and finds Weeks' corpse and Finch's cufflink. He checks the cell phone and discovers that Finch entered a tap code. He translates it and realizes that Finch said that he's at the train station.
Root comes back and wheels Finch to the train. However, she spots Reese entering the station. When she wonders how he found them and wheels Finch behind a pillar, Finch says that it proves that not all humans are bad code. Root waves to a guard while Finch backs up the wheelchair so that Reese can see him. She draws a gun and prepares to shoot the guard, and Finch lunges out of the chair, knocking her gun arm aside. Reese draws his gun and runs while Root slips away. Finch complains that he didn't intend for Reese to save him but Reese says that he owes him.
That night, Carter comes back and Fusco confirms that they got Finch back. She offers to buy him a drink and he accepts.
Finch goes back to the library with Reese and realizes that they now have a dog. He tells Reese that he owes him a debt, just as Reese gets a call. It's Root, who thanks him for finding Hanna and giving her a proper burial. She promises that she won't forget, and Reese tells her that if she comes at them again she'll be sorry. Undeterred, Root tells him to tell Finch that she'll be coming for him when the time is right. She hangs up and then watches as they Special Council's men take Denton's corpse.
Sam signs the high score with her new pseudonym: Root.