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The Machine goes through a series of events and conversations related to Root and her activities.

During a prison transfer in Illinois, one of the convicts, Billy Parsons, spots a body on the road and tells the driver to stop. One of the guards steps out to see who it is, and Root reveals herself, using a taser to incapacitate him. She does the same to the other guard and steps in, ignoring the flirtatious inmates and taking Billy with her.

She explains to Billy that he and her need to work together to "save the world", and gives him a phone with a recording of a German man's voice, telling him to learn the accent quickly. She also gives him a signature to memorize and a razor to shave, and later down the street, gives him a suit. Her assistant, Daizo, takes a photograph of them while Root explains that she saved him from the Tokyo police a month ago and he is now a friend of hers. They arrive at a secure building and Daizo hands Root a badge of Gunter Schmitz, a worker there. She gives the fake ID to Billy and tells him to go inside.

Billy signs a tablet with a fake signature and fakes a German accent to talk to a guard, who verifies his credentials. Root comes and tells them that they have to leave, right as the real Schmitz walks in.

Outside, Root thanks Billy for her help. She instructs him to sit across from a man named Arnold at his prison cafeteria and befriend him by mentioning his love for dinosaurs. She kisses him on the cheek and leaves while the police arrest him.

Back in New York, Root arrives at a bank and chats with the Machine about who her next number is, identifying various people standing out among the crowd. She spots a janitor named Cyrus Wells and invites him for breakfast.

At a diner, Root and Cyrus talk, and Root wonders why he isn't confused or worried. Cyrus explains that he believes that everything is part of "a greater plan", including her, but still asks what's going on simply for the sake of it. Root says that "her boss" wanted her to talk to him and they need to work on something together. Cyrus says that he now needs to go to the park, as it's part of his schedule despite weather conditions.

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In a snowy Central Park, Root watches Cyrus and then sits down next to Finch, who is reading a newspaper. He explains that he has also received Cyrus' number at the same time Root was spotted approaching him at the bank, and he believes Root is a threat to Cyrus just by coming in contact with him and her plans for him will get him killed. Root claims that she is protecting Cyrus, and also shows Finch her scar in her ear that she got from Control. (“Aletheia”) She warns Finch about Samaritan, and how its open-source nature can make it a weapon for Decima. She advises that he work to stop Samaritan from coming online rather than Cyrus, but Finch says that Cyrus was a multimillionaire and left Wall Street in 2009, suggesting she get more information from the Machine. Root assures Finch that Cyrus will be fine and sends him an advertisement for a testosterone pill, telling him "third from the bottom, fifteenth on the right, behind you" before leaving. Reese and Shaw appear next to Finch, who tells them to watch over Cyrus and Root while he figures out the meaning behind the ad.

At Cyrus' apartment, Root pours corn syrup in a frying pan and places a mirror next to the table, and Cyrus thanks Root for breakfast but wonders what she's doing. Root throws a breakfast bar to Shaw, who is standing on the street below. She says that she has things under control, and goes back in, packing up Cyrus' things against his request. She sees a picture of Cyrus with two people and asks who they are and what happened to them, but Cyrus refuses to tell her. A sniper fires at them but hits the mirror Root placed earlier, and Shaw goes after the shooter. Meanwhile at the Library, Finch discovers code hidden inside the ad Root sent him and realizes that the verbal clue she gave him was the location of a book in the Library. Finch finds it identifies the attackers: Vigilance - Collier and his men fire at Shaw.

In the apartment, Cyrus panics and tells Root, who has a pistol with her, that guns make him very nervous. Root instead puts paprika in the frying pan to create tear gas and leaves with Cyrus while Shaw fights the sniper. The Vigilance soldiers raid Cyrus' apartment and Reese attacks them. Finch, meanwhile, finds out that Vigilance is after Cyrus because his name appeared in a message sent out by Decima - Reese sees a car pull up with Greer inside. On the street, Root escapes with Cyrus.

On the street, Root picks up some eggs and gives them to Cyrus, picking one up and throwing it at a police car. She leaves the container with Cyrus and leaves while the police arrest him, thus taking him into safety. Reese watches and confirms Cyrus is safe. Finch informs Reese that Vigilance and Decima are after Cyrus likely because of his new job rather than his old one, and that a background check was recently run on him for unknown reasons. He also says he lost contact with Shaw, but Reese decides that they worry about Cyrus for now.

In a warehouse, Shaw interrogates the sniper, but more Vigilance men fire at her. Collier talks with her over the radio, saying she is probably a betrayed ex-government operative. He says he has locked down the exits and that he can offer her revenge on the government in exchange for information on Samaritan. He quotes Benjamin Franklin: "join or die".

Meanwhile at the NYPD precinct, Fusco calls Finch to confirm Cyrus is with him and cleared of charges. Finch says that he has sent him a rendezvous point to meet with Reese, but as they leave, Root appears, posing as an FBI agent to take Cyrus with her instead. Fusco doesn't let her but his captain arrives, forcing him to allow Root to leave. Fusco then calls Reese to explain the situation, and a payphone rings near Reese. He answers it and hears Root, who he tells that Cyrus is safer with him. Root says that they should trust her more and hangs up, sitting down with Cyrus at the diner.

She takes out her phone and opens the picture of Cyrus and his friends, imploring him to tell her who they are. Cyrus says that they are Sarah Lind and Alex Rice, his two best friends from college - they started a financial services firm following college and he helped them run it - they didn't bet on any markets, causing the firm to skyrocket during the Stock Market Crash. On April 4, 2009, a shooter opened fire inside Cyrus' office, and Alex and Sarah were killed while Cyrus escaped injured among others. He then decided to give his money away to charity and began cleaning its headquarters as a janitor. Root nervously assures him that his friends' deaths weren't "part of a plan", and leaves with him before the enemies arrive.

At Central Park, Decima hitmen get orders from Greer to activate a signal jammer, cutting off Root's communications with the Machine. Root tells Cyrus that they have to run, but Cyrus is grabbed by Decima men. Reese arrives and shoots at them, but Cyrus is still taken.

As the sky gets dark, Shaw continues to fight Vigilance in the warehouse and is eventually cornered. Collier appears and lectures Shaw on how America is "dying" and should be based around both privacy and principle, but the government is authorizing things like drone attacks, unauthorized interrogation and spying on the world, and that Vigilance plans to put an end to it. He offers Shaw a place in the organization for both revenge and a role in a "new chapter in American history", but Shaw says that how something is done matters just as much as what is done, and that policy makes Vigilance a group of terrorists - "she kills terrorists". She takes a metal pole and lashes out the men while Collier calmly leaves.

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Reese reports that he lost Decima's trail, but Finch says that he decoded a Decima message listing Cyrus as someone who has "retinal access" to a room belonging to a building he discovered is owned by a company called Maxwell Limited. He says that the company manages deliveries of liquid helium, and as he goes through what that could cool, Root appears and mentions "the fastest computer ever built" and that Maxwell is a front for an NSA lab. She gives him a paper which he realizes contains specifications for a micro-processor being stored in the room - the chip can activate Samaritan and because the government isn't willing to sell it, Decima plans to use Cyrus provide access to the room. Samaritan crashed because there wasn't a chip built to handle it's power - the chip was built two days ago and Decima needs the hardware to complete the project.

Reese says that they should worry about Cyrus since he is bound to be killed once he accesses the door into the room. Root declines, instead giving Finch patches for her ear that should be equipped with a computer chip, thus restoring both her hearing and her communication with the Machine. Finch asks whether she'll save the chip or Cyrus once the device is installed, but Root instead attempts to bring up points as to why Cyrus isn't of importance. She finally decides to come to the subject of Cyrus' friends, and says that a banking executive wanted them dead and hired someone to do so - she reveals that she was the one responsible. Her guilt is the main reason she doesn't want to save Cyrus, but she ponders how Finch "broke" the Machine so much to make it care about people. Finch said that it's the reason the Machine works and allows people to be helped. Root then says that many people will die when Samaritan is online, starting with him, her, Reese and Shaw. She says that everything she's doing is to save Finch, takes her ear device with her and leaves.

Root finds Dr. Carr, the best doctor she could find within the range of 250 miles. She demonstrates her enhanced environmental awareness to threaten him into fixing her ear.

At the Maxwell building, Decima reports to Greer that the building's security has been neutralized and that they are ready to take the chip.

Dr. Carr begins working at Root's ear while the Decima men take Cyrus with them into the building. They shove him towards the scanner, which verifies his identity using his eye. Greer approves and orders that they kill Cyrus.

Root's operation concludes and Dr. Carr wires up her device, preparing to start a hearing test. However, the Machine displays that the Analog Interface is now active and Root confirms she can hear now. She thanks the doctor and leaves.

In the lab, the Decima men gets instructions from Greer on searching the place. Cyrus, meanwhile, is prepared to be shot, but Reese arrives and fires at the Decima men. Fusco aids him, while Root arrives at the lobby and opens fire at the men guarding it - her enhanced hearing includes resistance to signal jamming. The Decima men locate the chip and Root arrives at the doorway, but when she hears gunfire from the other room, she decides to help Cyrus. She comes in and tells Reese that guns make Cyrus nervous - she comes to him unarmed and takes a bullet to the shoulder, but manages to escape with him. Reese goes into the other room, but sees that the chip has been stolen.

The Decima men report to Greer that they have retrieved the chip, and Greer declares that their work here is done. His workers douse their computer equipment with gasoline and leave.

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At Finch's safe house, Root and Cyrus talk privately in the balcony - Finch informs the team that he decided not to place a bug there. Root comes back and Cyrus prepares to leave, thanking them. Shaw looks at Root's ear work and gives her instructions on when the change the dressings. Root talks with Finch, saying that she didn't tell Cyrus about her involvement in his past since his belief of a greater plan helps him in life. Finch says that she isn't wrong about the Samaritan threat and offers to work with her in the future - Root simply says that she is preparing for a flight to Paraguay and that Fusco will take her to the airport. Fusco comes in and Root hands him a battery, saying that his smoke alarm will ring at 2:41 AM. She leaves and Finch looks on.

The Machine calculates the threats exposed by Samaritan's activation.

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