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The fact that it’s taking the Machine longer than expected to be fully operational has everyone on edge. Reese is restless because not only have there not been any new numbers, but also because homicides in the city are down - though, suicides are up. Root is stuck in the base because she’s a dead woman walking if she even peeks her head above ground without the Machine there to provide her with a cover identity. So, it falls to Reese and Finch to pick her up some supplies — black nail polish and fuzzy slippers, one for her, one for Bear to chew on — while they steal some servers to increase the Machine’s processing power.

With the servers installed, it’s time to wake up the Machine. Once she’s up and running, Finch and Root, who can’t understand why Finch ever boxed her up, take her for a spin. First, they have her identify Reese, who is standing in the middle of Times Square. She passes that test. Root’s eager to jump back into fighting Samaritan, but Finch insists that they start up the irrelevant numbers protocol first to make sure everything is in working order.

The Machine gives them 30 numbers. Some of them don’t really pan out because either the person isn’t an actual threat, a character getting shot in a play, or already dead. It seems as though the Machine isn’t processing context and unstuck in time. So, Finch decides to run a diagnostic to see how the Machine handles the team.

The Machine looks at everything they’ve ever done — especially Root and Reese, but also Finch — decides they’re threats, and takes steps to handle them. First, she locks Root and Finch inside the train car.

While Finch and Root are trapped in the subway car, Reese receives another number: Laurie Granger, who is visiting New York from Tulsa. It’s actually his lucky day because she walks into the precinct seeking assistance, except it turns out that she’s an assassin who was hired by, yep, you guessed it, the Machine. She chases Reese through the streets of Chinatown and into a nearby mall with a gun.

Meanwhile, the Machine turns on Root and starts attacking her cochlear implant each time Finch tries to touch the computer. He tries reasoning with her that they aren’t monsters, but then she shows them video of some of their past crimes. Not wanting to be a bargaining chip, Root tells Finch to knock her out by Desflurane with her instruction and then get to work on breaking into the Machine. That’s exactly what he does.

Now, Finch tunnels back into the Machine, and she shows him a video from back when he first built her and was explaining the difference between good and evil. He admits that things aren’t as simple as they used to be.

“These days, black and white just dissolve into grayscale,” he says. “I was wrong; I supposed everyone feels he’s the hero of his own story, but there are no heroes, no villains — just people doing the best they can… My only justification is that I did the best I could.” It’s an acknowledgement at just how complicated this entire war is. At this point, Team Machine is just doing the best they can to survive. 

Finch promises to never hurt the Machine again. “You are hurting me now,” she responds, and he realizes that she’s currently re-living all 42 deaths that occurred in her creation. That’s some serious trauma. The pain on his face is heartbreaking. But Finch has a solution to help the Machine: focusing on the numbers. He starts showing her everyone they’ve saved over the past four years so that those will anchor her in time. “There is good and bad in all of us, but this action, saving lives, it is a pure good. Help us. I can’t promise you we’ll always do the right thing, but we will do the best we can,” he pleads with her.

The Machine re-contextualizes all of her data and frees Finch from the subway car. At the same time, Reese finally manages to get the upper hand against the assassin that’s after him. Oh, and Fusco, who was dealing with a legit number, saves a family from the Lithuanian mob. 

Towards the end, one of the numbers Reese had earlier was Jeff Blackwell, an ex-con who was just released from prison and is trying to make an honest go at life. Unfortunately, he’s having trouble finding steady employment. Well, that is until he goes into an employment office seeking a job and is recruited by Samaritan, who starts analyzing his propensity for violence.

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