Sam is sleeping in her apartment when she wakes up at a slight noise. Before she can do anything, Root tasers her unconscious.
Two men on the phone discuss a third one getting too close, putting their organization risk. They agree to vote about what to do with him.
When Sam doesn't respond to Finch's call within eight hours, Finch sends Reese to check on her apartment. Finch is busy at the apartment of a compulsive hoarder, Marcia, working undercover as a new partner with estate investigator Timothy Sloan. Timothy investigates people how have died to learn who their next-of-kin are. Timothy finds a detective novel belonging to Marcia and admits that he wanted to become a police detective, but he couldn't shoot straight. They finally find a box of slides confirming that Marcia had a sister. Meanwhile, Reese informs Finch that he found taser confetti in Sam's apartment, indicating that somewhat abducted her.
Sam wakes up and finds herself plastic-cuffed to the steering wheel of a car. Root is in the passenger seat and apologizes for abducting her, but explains that The Machine told her to team up with Sam. When Sam notes that The Machine only gives relevants and irrelevants, Root informs her that The Machine is evolving and has created a new type of mission. Root then cuts Sam free and invites her to take out a gun in the glove compartment. Sam grabs the knife instead, puts it to Root's throat, and asks why she shouldn't kill her. Root says that The Machine told her the date when Sam's father died in a car crash, and that Sam knows The Machine is never wrong. Now The Machine wants Root soave it, and all of the innocents that it protects. Sam reluctantly agrees to go along with her, but warns that once the mission is over, so is their truce.
That night, Finch takes Bear and follows Timothy as he breaks into an apartment. He informs Reese that Timothy is looking into the death of Jason Greenfield, who died of a heroin overdose two weeks ago. Meanwhile, Reese has broken into the building across the street from Sam's apartment, knocked out the guard, and accessed the security footage. He confirms that Root abducted Sam and warns Finch, who tells him to find them. Meanwhile, Timothy searches Jason's apartment and takes out a watch from a drawer. He gets the drop on Finch, who asks why he's there, and Timothy shows him an engraving on the watch confirming that Jason was his foster brother.
Timothy explains that his parents adopted Jason. Jason was a hacker and after he left home at 18, he became increasingly obsessed. He finally disappeared until Timothy saw the report about his death. The investigator insists that Jason never used and points out all of the sellable items in the apartment that would be gone if Jason had needed money for drugs. There's no computer in the apartment, but Timothy has found a flash drive in the microwave that someone tried to destroy. Finch scans it on his laptop and finds a small bit of information in an email saying that Jason was worried someone would leave him if he tried to leave an organization. Timothy finds an address on a piece of paper in Jason's jacket and Finch confirms that it belongs to a storage unit, even though Jason didn't have a storage unit.
The next day, Laskey is out collecting protection payments for HR and makes a pickup from a deli owner named Morozov. Carter is watching him and he comes over to meet with her. She tells him to deliver it to HR as usual and find out where it's going, reminding him that she can frame him for murder at any time. Carter asks about Morozov and Laskey insists that the deli owner is simply paying HR as a token of his loyalty and appreciation. She warns him that HR will soon show Laskey what they want in return for his loyalty.
Fusco finds the car that Reese stole from the mental hospital and calls in Reese. A driver reported that he saw Root and Sam steal a medical transport van, and they figure the two of them are working together. Meanwhile, Finch tells Reese about Jason's murder by a secret organization and tells him to focus on finding Sam. Finch then has coffee with Timothy, who confirms that Jason rented the storage unit under an alias and paid with cash up front, and was one of several people who visited it. The day after Jason died, the others went back and scrubbed the place down with bleach, removing all forensic evidence. Finch checks for other storage units rented with cash find finds one to another alias. Both aliases are American generals, and Finch and Timothy figure that the same people are involved.
As they walk down the street, Root points out a statue of a horseman and tells Sam to think "impact" the next time she sees it. She then tapes a manila envelope beneath a park bench, telling Sam that is' insurance. They descend into the sewers and Root has Sam use an improvised blowtorch to cut through a grille. When Sam asks for an explanation, Root admits that she doesn't know and that she's just following orders from The Machine.
That night, Timothy, Finch, and Bear go to the second storage unit. There's nothing inside but Finch tells Timothy to get a UV light out of his car that he uses in his investigations.
After they finish in the sewers, Root leads Sam to an apartment and they break in. They wait until a man comes in and tries to run. Sam attacks him and the man is clearly a trained fighter. Root finally tasers him unconscious and Sam realizes that they're at a CIA pickup site. Root calls a CIA number and gives a number and password provided by The Machine. The contact tells her that they should have the package ready for pickup at 0800. When Sam wonders what the package is, Root says that she's the package.
At the storage unit, the UV light reveals that the walls are covered in writing. Finch realizes that it's a message center for people to contact each other. As they look around, Timothy notices a sprinkler pipe that is on its own line, and a motor attached to the door. Finch spots a camera and realizes that it's a trap, just as the door slams down under remote control. Gasoline sprays down from the sprinkler and an electric igniter starts up. Reese arrives and breaks down the door, and they get out just as the gasoline ignites, blowing up the place.
The next day, Finch deciphers the coded messages from the photos he took and confirms that one of the men responsible is Peter Collier, a member of the anti-surveillance group who killed data broker Wayne Kruger. Jason hacked government websites to release top-secret information and became a member of Collier's group, but had second thoughts after they murdered Kruger. When Jason tried to get out, Collier's group killed him. Finch figures that the group will come after Timothy next because he knows too much. Going over the coded messages, Finch realizes that they are encrypted and need a long text string like a book or letter to decipher them. Reese heads out to Jason's apartment to search and Timothy insists on going with him, pointing out that he's a trained investigator. Reese and Finch agree to let him tag along.
As two transport agents arrive at the CIA apartment, Root gives Sam a number from The Machine. When the agents come in, Sam gives them the number, confirming that she's a CIA agent with authority to accompany them with Root as their prisoner.
Simmons calls to tell Laskey to go to the deli. When the young officer gets there, he discovers that it's closed. Simmons and a local contact are waiting in the alleyway, and Simmons calls Laskey over. He explains that Morozov was skimming on his payments, and that the shopkeeper wasn't loyal to them. Laskey objects but Simmons says that they want fear, not loyalty, like the local man who ratted Morozov out. The older cop then tells Laskey that Morozov went for his gun when he confront him, and gives Laskey a new assignment: bury the deli owner's corpse six foot deep. As they talk, Carter continues secretly taking photos.
Sam accompanies the CIA agents to a holding cell at a CIA black site. Root gives two identification words to Sam before she's locked up in a cell. The chief interrogator, Nick Breckenridge, comes over and tells Sam that they're prepping to move the prisoners as part of a 7-hour cycle so that they can question them indefinitely. His walkie-talkie goes off and Breckenridge complains that they've been malfunctioning. He asks for the identification phrase and Sam gives him what Root told her earlier. She doesn't have the final authentication number and Breckenridge eyes her suspiciously. However, when his radio goes off again thanks to The Machine, Sam gives him the remaining information that Root passed on, and he uses it to shut off the static. Satisfied, Breckenridge tells Sam that she can leave with the team for the next black site with the prisoners.
The next morning, Reese and Timothy search Jason's apartment and Timothy finally remembers that Jason always hid things in the heater vents. Inside they find a book on the American Revolution and Reese sends images of the pages to Finch. He uses the book as an algorithm to decipher the messages, while armed men burst into the apartment. They toss a flash-bang grenade, stunning Reese long enough for them to get to their van with Timothy. Collier is waiting for them and they drive off as Reese staggers out. Reese calls Finch to give him the news and Finch tells him that he's deciphered enough of the messages to confirm that Collier's group learned that Jason had gone to the CIA, who helped fake his death. The group is planning to intercept the CIA transport van with Jason inside and kill him.
At the CIA black site, CIA agents toss Jason into the cell next to Root. She calls to him by name and says that she knows the Feds screwed him over when they broke his deal after he came to them. Jason wonders who she is and Root confirms several infamous hacks that she performed. As she works a link in the cage separating them, Jason tells her that Collier's group, Vigilance, learned about Kruger through him. It was Collier who convinced the group to authorize Kruger's death despite Jason's objections. Breckenridge returns and Root tells Jason that she's there for him.
The CIA team load the prisoners aboard the transport van. Once they're alone, Root starts cutting her plastic ties with a link from the cage.
Finch tells Reese that the messages show that Vigilante plans to take Timothy with them on their way to kill Jason. The message info contains the anticipated location of the ambush and Finch passes the information onto Reese.
As Collier and his team drive to the ambush site, Collier wonders why Timothy is looking for Jason. Timothy refuses to reveal that they're foster brother, and Collier respects his desire for privacy. However, he warns Timothy that they had to dispose of him when he learned too much about Vigilance. The group voted to kill Timothy, and all Collier can offer Timothy is a quick death if he tells them about Finch and Reese. Timothy has no idea why they're helping him, and Collier tells the investigator that his foster brother Jason is alive. The Vigilance team arrive at the ambush site and Collier pistol-whips Timothy unconscious.
Root finishes cutting through her bonds.
Reese arrives at the ambush site, which is near a statue of a horseman. He spots Collier's van and the CIA transport van approaching. Sam, driving up front, sees the statute and remembers what Root said earlier about "impact." A vigilance member posing as a homeless man wheels a shopping cart out in front of the van, and the paint bomb inside explodes. Blinded, Sam drives the transport van off the road. Collier and his men approach, but spot Reese and open fire.
Root leaves the van via the back door and goes to the bench where she taped the envelope earlier. Inside is a gun and an earbud. Once she reestablishes contract with the Machine, Root gets Jason out of the van. Shaw wakes up and looks for Jason, while Reese arrives and looks for Timothy. Meanwhile, Timothy wakes up and catches up to Collier, who grabs him and uses him as a human shield when Root opens fire on him. Unable to get a clear shot, Root takes Jason away. Sam arrives just in time to see her go down in the sewers.
After leading Jason to the sewer grille that Sam cut open earlier, Root gives him a flash drive with a new identity and a passcode to an account containing $2.5 million. She tells Jason to make his way to a bar in Cartagena, but admits that she has no idea why. All she can assume is that Jason is necessary to The Machine. As Jason makes his escape, two of the Vigilance soldiers arrive. Root tries to fire but realizes that she's out of bullets. Before they can kill her, Sam arrives and takes them out. She asks Root if they've completed their mission. When Root says that they have, Sam punches her unconscious.
Reese tries to get a clear shot at Collier, who still has Timothy. When Collier quotes Benjamin Franklin, Reese points out that he has a thing for the American Revolution. Collier says that it may be time for a new American Revolution, and then shoots Timothy in the leg, severing the femoral artery. He tells Reese to choose and then drives off in the van. Forced to save Timothy's life, Reese tends to the wound and has Finch call in an ambulance.
The next day, Simmons calls Laskey and confirms that he buried the deli owner. Laskey then meets Carter in their car. When she wonders how he slept after burying Morozov, Laskey explains that his real name is Mikhail Lesnichy, and he's one of twelve Russians on the force. Carter realizes that HR is seeding the department with Russians loyal to them, cementing their relationship with Yogorov. Laskey admits that he doesn't know specifically what HR intends to do with the money, but they're stockpiling it for something big. Carter warns her partner that things will get worse, but Laskey asks her what is worse than burying a friend.
Finch and Reese meet Timothy outside the hospital and he thanks them for their help. Jason calls and tells Timothy that he's on a secure line, and thanks him for everything he's done. He assures Timothy that he's his real family, and Timothy promises to hold onto his watch until they meet again. Once Jason hangs up and Timothy leaves, Reese tells Finch that they'll have to keep watch on Timothy in case Vigilance goes after him again. Finch is more worried about The Machine, pointing out that it sent both them and Root into battle but with different goals. When Finch brings up Root, Reese wonders what they're going to do with her.
That night, Finch visits Root, who is locked up in a storage cage in the library. She has an ankle monitor is on, but warns that she has to make contact with "she." Finch notices the use of the feminine pronoun, while Root realizes that Finch has rigged the cage up as a Faraday cage to keep her from contacting The Machine. Root warns him that The Machine will be angry at him, and that Finch doesn't want an omniscience computer mad at him. Finch suggests that Root is right where The Machine wants her, and leaves on that note.