The safe house is attacked, Elias brings Finch to the Brighton Beach high-rises, and brokers peace between the rival gangs. The high-rises are attacked as well, Elias and Finch try to escape, reach the getaway car, but find the driver dead. Once more, they are ambushed by Samaritan operatives, Elias kills them in self-defense, ushers Finch into the backseat, and, while protecting him, is fatally shot in the head by an operative.
Samaritan operatives kill Elias and take Finch to see Greer. He is told one day in the future, even if he doesn't see it yet, he will work for Samaritan by his own accord. As Zachary puts Finch in the back of a car, Shaw and Root attack. Finch and Root escape as Shaw draws the Samaritan operatives' fire.
On the run, Finch and Root are shot at by Jeffrey Blackwell. Root sees him, makes an evasive maneuver to protect Finch, and is shot instead of him. Soon after, the two are stopped by policemen. Finch is arrested; Root is taken to the hospital in critical condition.
In police custody, Finch is interrogated by an FBI officer who reveals Finch's fingerprints have been found on 15 crime scenes over the past 5 years, and he has an open treason case from 1974. Though all of electronic copies of Finch's criminal records are gone, a hard copy of his treason file still exists in storage in Washington, D.C. After the interrogation, the Machine contacts Finch who asks her to break him out of jail. The Machine stages a prison break, letting hundreds prisoners escape.
During Finch's interrogation, Root succumbs to her injuries. The Machine selects her voice to be its own.
Defending his actions in the 1970's, Finch says, "...a sitting President had authorized assassination squads in Laos, and the head of the FBI had ordered his men...to conduct illegal surveillance on his political rivals." He is referring to The Phoenix Program, a CIA-run operation using torture and assassinations to destabilize the Viet Cong during the Vietnam War, as well as FBI Director J. Edgar Hoover's activities, an element of the Watergate scandal. The sitting president was Richard Nixon.
Potter's field is referenced in a comment Root makes, that if Harold won't permit the Machine to help them more actively, they will "end up the most principled corpses in Potter's Field," meaning they will be buried as unknowns, in a common mass grave of anonymous and forgotten people.
Bloopers and Continuity Errors
When Elias is shot, the blood on his head is already dry, this is impossible.
"New Dawn Fades" - Moby (Root and Shaw's battle with Samaritan operatives)
"The Day the World Went Away" - Nine Inch Nails (end of episode)
Harold's intro ID in this episode is ID.008/2720.10, John's ID in Season 2 intros. Harold's ID was ID.005/3020.06.
In this episode, Fusco is assigned, for the first time, a yellow box in the intro and labelled "Primary Asset" instead of "Secondary Asset".
"I have played by the rules for so long. ... No, not your rules. You work at the behest of a system so broken that you didn't even notice when it became corrupted at its core. When I first broke your rules, a sitting President had authorized assassination squads in Laos, and the head of the FBI had ordered his men, you, to conduct illegal surveillance on his political rivals. Your rules have changed every time it was convenient for you. I was talking about my rules. I have lived by those rules for so long, believed in them for so long, believed if you played by the right rules eventually you would win. But then I was wrong, wasn't I? And now all the people I cared about are dead or will be dead soon enough. And we will be gone without a trace. So now I have to decide. Decide whether to let my friends die, to let hope die, to let the world be ground under your heel all because I played by my rules. I'm trying to decide. I'm going to kill you. But I need to decide how far I'm willing to go. How many of my own rules I am willing to break... to get it done." (Finch, first to the Fed agent, then to Samaritan)
"You created me, I can do anything you want me to" (The Machine, to Finch)
"I got a feeling Finch isn't here anymore. Samaritan didn't want him dead, at least not if they could capture him." (Reese, to Shaw) "Then why did his number come up?" (Shaw, to Reese) "I think it was warning us about what he might do to them..." (Reese, to Shaw)
"We're not living. We're surviving" (Root, to Finch)
"Harold has a weakness." (Shaw, to Root) "We all do." (Root, looking at Shaw)
"It'd be nice if we could go back. I guess none of us... has the life we want." (Shaw, to Root) "Actually Sameen, I've been hiding since I was 12. This might be the first time I feel like I belong." (Root, to Shaw)
"Schrödinger said that at its base level, the universe isn't made up of physical matter; just... shapes. I thought that might make you feel better. ... A shape, you know? Nothing firm. What it means is the real world is essentially a simulation anyway. ... I like that idea. That even if we're not real, we represent a dynamic. A tiny finger tracing a line in the infinite. A shape. And then we're gone." (Root, to Shaw)
"Listen, all I'm saying that is if we're just information, just noise in the system... we might as well be a symphony." (Root, to Shaw)
"Listen. I know you have apprehension about what the Machine is, about what She will become. And I trust you, Harold. I walked in darkness for a very long time until you guided me to light, and I wouldn't change any of it. But we're not going to win this way. We can't afford to lose. When the time comes, you'll know what to do. And I know this is an ugliness you never wanted, but sometimes you have to fight a little." (Root, to Finch)
"I'm fine Harry. I'm just fine. Keep your eyes out, I need to drive." (Root, to Finch. Her last words of the series)
"That's supposed to make me feel better? I'm a shape?" (Shaw, to Root) "Yeah. And darlin', you've got a great shape." (Root, to Shaw)