- Detective Carter and Mr. Reese go to Texas to look into Root's past. Root shows to Finch that the people who bought his Machine are evil. Mr. Reese finally finds Finch.
- While Reese leaves his newly acquired dog, Bear, with Fusco who will continue to investigate Alicia Corwin's death in New York, Reese and Carter head to Bishop, Texas to follow a lead about Root, and hopefully a still alive Finch who also hopefully did not need to divulge how to access the machine to Root in order to stay alive. Reese believes that Root's real name is Hanna Frey, who went missing in 1991 at age fourteen. In the eyes of the authorities, Hanna, who spent the evening at the library the night she went missing and was reported to have gotten into a man's car after her stint at the library, is presumed dead. Reese and Carter manage to speak to many of the still alive players associated with Hanna or that evening, including Hanna's father, Barb Russell the librarian, Sheriff Landry, and Cody Grayson, a boy at the library that night who is a suspect in Hanna's disappearance since he had previously followed her home. The information they are able to collect - including from some junk mail addressed to Hanna, and from Finch concerning his investigation - leads Reese and Carter in some unexpected directions. Meanwhile, Root continues to use the hot button issues to get the information she wants about the machine from her now two captives, Finch and Denton Weeks.—Huggo
- Reese and Carter travel to Texas to investigate the disappearance of the fourteen-year-old Hanna Frey in 1991 since Reese believes she is Root. He leaves his dog Bear with Fusco and asks him to continue to investigate the death of Alicia Corwin. Reese steals the file of Hanna Frey from Sheriff Landry's office and soon they find flaws in the original investigation. They interview Hanna's father and the librarian Barbara Russell and soon they discover what happened to Hanna Frey. Meanwhile, Root tortures Denton Weeks since she wants access to The Machine. When she finds that Weeks will not help her, she shots him and dopes Finch to travel with him by train.—Claudio Carvalho, Rio de Janeiro, Brazil
- A flashback to 1991 and a 911 call placed about Hanna Frey, "the girl who's gone missing."
In present day Carter tells Reese that in '91 a 14-year old Hanna Frey walked out of a public library in Texas and was never seen again. Reese thinks this must be Root and if they can find out what happened to her they'll be able to find Finch. Reese wants to go to Texas, telling Fusco to stay in town, dog sit and figure out who has been interfering with the case.
"Special Counsel" (Jay O. Sanders) calls Hersh (Boris McGiver) and instructs him to figure out how the Corwin case got to New York.
Reese and Carter rent a hotel room in Texas.
Carter talks to local law enforcement about the Frey case, telling the sheriff (Loudon Wainwright III) a similar case has arisen in New York. The sheriff isn't willing to help much, but Reese steals the file while she's in there. There was a 911 call that night from someone who saw Hanna get in a car, but nothing checked out.
Root assures Finch that she'll eventually get access to the Machine. She has Denton Weeks (Cotter Smith) tied up and says only one of the men will be walking out of there.
Reese and Carter speak with librarian Barbara (Margo Martindale), which leads us to another flashback from that night: Hanna was playing a computer game near closing time. She checked out a few books and left. Barb tells them Hanna's father is still in town.
Hanna's father tells them he believes a man named Cody Grayson was responsible for her disappearance. He tells them he occasionally gets junk credit card mail in Hanna's name.
Fusco tells Carter there was no hotel key on the slain Alicia Corwin's body.
Reese finds Cody in a bar, drunk during the middle of the day. Almost incidentally, this requires Reese beating up half the bar, good ol' boys who taken exception to a stranger in a suit. One of the antagonists is propelled headfirst and horizontally through a window and out onto the sidewalk. (Where have we seen this before?) Cody says he has no idea what happened to Hanna. Carter shows up and tells Reese that Hanna had opened up a bank account in 1993, two years after having gone missing.
Root is using enhanced interrogation techniques on Weeks. He continues to tell her he has no idea what the "Machine" is. Finch asks Root, "What happened to you?" She gives Weeks some sodium pentothal. When she leaves the room Weeks tells Finch they have to make sure Root does not get access to the Machine.
Carter and Reese find out Hanna's bank account at one point had $100,000 in it and the money was withdrawn in cash over a period of three weeks. Carter says it was stolen electronically from a drug dealer. A local named Trent Russell was a signatory on the account. Russell was at the library the night Hanna disappeared.
Russell turns out to have been Barbara's husband who had died 15 years earlier. She tells them Russell was attacked and shot to death. The authorities believed it looked drug-related. Reese finds a car in the garage. It has the same license plate as described in the 911 call from that night in 1991. Reese thinks Root set Russell up to be killed by the drug dealers she stole from.
Weeks tells Finch that if he doesn't help him get free they'll lose the Machine. Finch is able to kick him a knife, conveniently left on a table between them. Weeks gets free just as Root comes back and they fight with Weeks subduing their captor. Weeks then picks up the gun Root had dropped and says to Finch "I want to know what you know."
Carter finds 16 copies of "Flowers for Algernon," the book Hanna checked out that night, hidden in the Barb's room. One arrives every year on the date of her disappearance. There is a receipt from a Seattle bookstore in the most recent copy.
Weeks asks Finch whether or not Root can get to the Machine. He says the Machine can not be altered remotely, meaning as long as it is hidden it is safe. At this point Weeks is going to shoot Finch, but Root, who'd been feigning unconsciousness, zaps him with a stun gun and shows Finch that the pistol she "dropped" was unloaded. She loads it.
The 911 call is played for Barbara, who admits recognizing the caller as a girl named Sam.
In a flackback Hanna recommend "Flowers for Algernon" for Sam. At the time Sam told Barbara she thought it was Russell in the car, but Barbara scolded her for even thinking such a thing. Barbara reveals that Russell had the back patio re-done two weeks after Hanna had disappeared.
Reese finds the account associated with the book purchase. It leads him to a credit card registered to Kelly Dyson that was used a few hours ago in Maryland.
The patio is dug up. A body is found next to a backpack with "Flowers for Algernon" inside.
Root had planned for Finch to set Weeks free and beat her up, seemingly to show him what Weeks is really like. Regardless, Finch says he'd rather die than give her the Machine.
Carter comes back to the motel. He tells her about tracing Root and she tells him Root must be Sam, not Hanna.
Another flashback to that night. Sam, clearly a crypto-computer wiz, watches Hanna get into Russell's car.
Fusco is able to eavesdrop on Hersh's call with Special Counsel and hears the latter instruct him to find the home of the woman Weeks kept on the side.
Root injects Finch with a sedative and asks Weeks once again where he sent the Machine. He gives her information about a train. As this is happening Finch is pressing keys on the cordless 'phone with his toes. She shoots Weeks twice and after chiding Finch for thinking she'd leave any 'phones connected, leaves with her prisoner invalided in a wheelchair.
Fusco gives Reese the name of Weeks' girlfriend. Reese instructs him to do a property search.
Root and Finch arrive at a train station.
Reese gets to the house and finds Weeks' body. He looks at the 'phone and starts to work out the tap code message Finch had left for him. It spells out "train station."
Reese gets to the station. Root notices him and, as punishment, prepares to shoot an innocent man. At the last moment Finch knocks her out of the way, but Root is able to escape.
Finch tells Reese "I owe you a debt." The 'phone rings. It's Root and she thanks Reese for finding her friend Hanna. She says to tell Finch she'll be in touch "when I'm ready."
A flashback to 1991 in the library reveals that Root's pseudonym comes from the game Hanna enjoyed playing on the library computer.
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