The Machine on its team, monitoring the police in Colorado arresting Reese and Fusco, and Control and her government agents capturing Finch, Sam, and Arthur Claypool.
Control informs Finch that now that she has him, he can tell her where The Machine has been moved to, and doesn't believe him when he says that it moved itself. She says that if she can't get the information about The Machine from him then she'll get the two missing drives from Arthur eventually. Control tells Sam that it's been a thrill watching her work and then orders her men to kill Sam and Finch. Root bursts in, firing, and Sam uses the distraction to take out her captor and break free. Between rounds, Root gives Sam one of her guns and the two women cover Finch and Arthur as they escape to an elevator. Hersh shoots Root in the arm before she can make it, and she tells Sam the elevator code. The others escape and Hersh smashes Root's cell phone and then knocks her unconscious.
Down below, Sam breaks into a car and Finch hotwires it. They drive off just before Hersh can arrive to stop them.
In Iowa, Harold is packing for his father, who doesn't remember that his son is taking him to an assisted-care center, The Pines. Harold tells him that he'll take care of him later and glances over at the memory circuit he's created. He tells his father that it's more of a friend than a machine, and that one day it will protect Mr. Finch. Harold's father promises to tell everyone about his son the genius.
Finch drives to a bank and explains to Sam that even though the drives are broken, Control can have someone fix them if she can obtain them. Until then, they have to avoid both Control's people and Vigilance, the people who were interrogating Arthur at the hospital. As they walk toward a nearby bank, Arthur wonders where Nathan is and Finch finally tells him that Nathan isn't coming. Arthur realizes that his friend is dead and then tells finch and Sam that he faked memory loss to keep Control from torturing him. He tells them that the drives are with a friend of his and Finch's and goes into the bank.
Control takes Root to a government safehouse and offers to help her escape from Finch and Reese. She realizes that Root has administrative access to The Machine and demands the code, but Root refuses, saying it would be like giving a child the keys to a jet. Unimpressed, Control injects her prisoner with a tranquilizer.
In Colorado, Reese wakes up and tells Fusco that it was stupid of the detective to pick a fight with him. Fusco tells his cellmate that the sheriff could care less about Fusco's badge and is going to keep them locked up.
In New York, the trio go into the bank and Arthur explains that he put the two drives in a safe deposit box. He removes the key from his medical alert medallion and give sit to the bank manager, identifying himself as Rudiger Smoot.
Control shoots Root up with an amphetamine and explains that they'll keep alternating tranquilizers and amphetamines until she tells them what they want to know or her heart explodes. As Control prepares to give her another injection, Root tells her that The Machine is beyond her reach. Control gives her another shot of a sedative and Root passes out.
Ms. Wallace takes Finch and Arthur to the safe deposit vault while Sam works out that Arthur's fake ID, Rudiger, was the name he gave to the Vigilance interrogator at the hotel. She spots Vigilance taking out the security cameras with laser beams and warns Finch, telling him that she'll slow down Collier and his group as they draw their guns and order everyone down. The police pull up outside along with Hersh and his team, and Hersh takes charge of the crime scene. Collier goes to the vault before Finch can escape with his friend, and he has no choice but to close the vault door. As he slams it shut, Collier gets off one shot, wounding the bank manager in the leg.
In Colorado, Fusco says that they should head home but Reese tells him that he has no home and that all they've been doing is delaying the inevitable by saving Numbers. He figures that Fusco will eventually go back to his crooked ways and nothing has changed. Disgusted, Fusco tells Reese that Carter was better than either one of them, and he isn't giving up even though she's dead. He then calls to the waiting sheriff and the man releases them. As Fusco leaves, Reese tells him to thank Finch for the job, and Fusco says that he hasn't heard from Finch and their friend is probably in danger. However, the detective says that there's no point helping him because it's just delaying the inevitable and walks off.
Finch maintains contact with Sam via radio and she tells him how to treat the bank manager's wound. She admits that she can't take out Collier and his men because they're the only thing keeping Hersh's team from storming the bank. Finesse tells her to use some finesse like Reese would and Sam tells him that she has plenty of finesse.
Hersh calls Collier on the phone and says that he'll let the Vigilance team walk away in the next sixty seconds. After that, he'll wipe them out. Collier knows that Hersh will kill him and his men no matter what and promises to obtain the Samaritan drives and exposes the government privacy abuses to the public.
Arthur opens the safe deposit box and removes the two drives, as well as a handwritten noted dated February 2005. It's in Arthur's handwriting but Arthur doesn't remember why he wrote it.
As she writhes in pain, Root begs The Machine to help her. When Control continues her interrogation, Root laughs despite her agony and tells her interrogator that she is the interface, and to give her a phone if she wants to talk to The Machine. Control takes out a cell phone but then puts it down on a table, and Root tells her that The Machine both looks out for her and uses her. Control accepts that she's telling the truth about being a point of contact, but informs her that she's going to perform a stapedectomy on the bone in her right ear to disable her hearing there. As she begins cutting, Control asks Root why she's a prisoner if The Machine loves her so much.
Arthur finally works out that he wrote the note one day before Samaritan was shut down, and realizes that he solved the AI problem that day... and that Samaritan was a true sentient AI.
Harold is unable to get the processing power he needs for his memory circuit. He finally uses a whistle to hack into the government computers to get the necessary power.
As Hersh prepares to move inside, Collier calls to give Finch one last chance, but Finch hangs up on him. Meanwhile, Arthur looks at the drives and Finch advises him to destroy them before the fall into the wrong hands. He finally tells Arthur that he and Nathan used Arthur's ideas to build their Machine. Arthur refuses to destroy his child, saying that it's life, even though Finch warns that The Machine hasn't made the difference that he hoped. Finch again warns his friend that Control will use Samaritan to enslave others, and Arthur finally says goodbye, promises to remember it, and then smashes the drives.
Sam tells Finch to take cover and he gets Arthur to cover. As Collier blasts in through the door, Sam detonates her pipe bomb, blowing a hole into the sewers. Two Vigilance men enter the vault and prepare to kill Finch and Arthur, but Sam takes them out and gets the two men out.
Hersh and his men burst into the bank, taking out Collier's men. One of the SWAT shooters fires on Sam, who sends Arthur and Finch down the stairs while she takes out her opponent. However, Collier and four of his remaining men capture Arthur and Finch, and force Sam to surrender. Once Arthur tells him that he destroyed the drives, Collier figures that having Arthur will be sufficient. He tells his men to dispose of Sam and Finch, but two SWAT officers open fire from the stairway. Collier manages to escape with two of his men while the officers reveal that they're Fusco and Reese.
While the team escapes into the sewers, upstairs Hersh and his men surround the last Vigilance agent, Heyward. He talks about replenishing the tree of liberty the blood of patriots and tyrants, and then detonates a hand grenade as Hersh dives for cover.
After killing the guards, Root ties Control up, plugs in a cellphone, and asks The Machine what it wants to do with her prisoner. The Machine speaks through Root, asking why Control has done what she has. Control insists that The Machine belongs to her, but The Machine says that it doesn't belong to anyone. It warns her that it knows the address of the only thing she loves, and that it guards it like it guards Control. When Control asks what it wants, The Machine that it wants to save her.
The next day, Finch takes Arthur to a private hospital. Arthur says that he's glad Finch built The Machine but admits that his memories are fading. Finch tells him that his memories are still there, just hidden. Root calls and points out that if they had worked together, then Samaritan would still be "safe. Finch assures her that Arthur destroyed the drives, but Root tells him that the real bank manager was found dead in a closet, and was killed before Finch got to the bank.
Root has Finch put Arthur on the line, and she tells the patient that The Machine has something to send him on his way. The TV that Arthur is watching brings up footage of Arthur's wife, his best times with her and at MIT with Finch.
Harold goes to see his father and warns him that men will soon come to talk to him, and will claim Harold is a traitor. He assures his father that he isn't, but his father no longer remembers who Harold is. Harold looks outside the window and sees a bird, and asks his father what it is. As Mr. Finch struggles to remember, a government car pulls up outside. Harold gives his father a book of birds, kisses him, and leaves.
Reese goes to the library to see Finch, who explains how The Machine helped Root escape. He welcomes Reese home, but Reese says that he only came back to protect Finch. Reese no longer trusts The Machine, pointing out that blindly trusting it got Carter killed. He wonders if The Machine cares who matters and who doesn't anymore, and says goodbye. Finch says that he can't go but Reese walks away.
That night, the fake bank manager meets with her employer: Greer, with Decima. He confirms that she didn't check the contents of the two drives and that she didn't tell anyone about them. Once he's satisfied, Greer shoots her dead. As he walks away, Greer promises Samaritan that it is destined for great things.