An organ-transport driver, Eric Mathers, is forced to pull over when a SUV gets out. Two Japanese mobsters force Mathers out and the leader, Murakami, says that their boss needs the liver. Sam, dressed as the other driver, steps out and shoots the first hijacker. When Murakami tries to take Mathers hostage, Sam shoots the hijacker through Mathers' jacket, killing him. Mathers tries to thank her but Sam ignores him and walks off. Finch suggests to her over the earbud that she work on her social skills and invites her to come by the library for a cup of tea, but Sam says that she has other business.
That night, Simmons and Tierney meet with Russian mobster Peter Yogorov. They want Yogorov to assemble all of the players together to meet with their boss. Meanwhile, Carter is nearby, covertly taking photos of the meet. When she goes back to her car, she finds Reese waiting for her. Reese tells her that he and Finch have known about her private project to bring down HR, and wonder why she isn't using the evidence she has to take down half of HR and make a deal to get the others. Carter informs him that she's after the unknown boss, and that she won't go to the authorities with her evidence until then. She explains about the new meeting between HR and the Russians, and assures Reese that if she needs his help then she'll call him in.
The next day, Reese and Sam meet Finch at the library. Finch explains that he doesn't have anything on their new Number because she doesn't have a digital footprint. The Number the Machine provided is a USCIS alien registration number, and they're looking for an immigrant. The registration number is for a woman, Genrik Zhirova, and she lives in a housing project. Sam and Reese go there and Sam poses as a customs officer. The man owning the apartment, Vadim Loginov, calls for Genrika and then goes back to his video game. Sam notices that there are several packets of drugs strewn about.
A ten-year-old girl comes out and explains that she's Genrika. Gen tells Sam that her mother Oksana is in prison in Russia and she never knew her dad. Her grandfather Yuri brought her to the U.S. but he died eight months ago and left her with her third cousin, Vadim. Vadim speaks up, complaining that Gen is always sneaking around, taking photos, and Gen says that she plans to be an international spy when she grows up. She wonders why Sam is there instead of her usual customs officer, but Sam realizes that Gen is bluffing and there is no customs officer. Gen tells Vadim to pay the rent and leaves for school, saying that she's late.
Finch checks Gen's record and discovers that her mother was imprisoned for protesting the Putin regime. As Sam follows Gen, Finch suggests that Sam might have been nicer dealing with Gen. Meanwhile, Gen uses counter-espionage tactics to spot Sam following her, much to Sam's surprise. Reese takes over following the girl while Sam goes back to recon the housing project. Finch switches to a private channel to talk to Reese, suggesting that they keep Sam away from Gen so she doesn't frighten the girl. Much to their surprise, Sam butts in on their private channel and tells Finch that she has the library bugged, and can hear everything they're saying.
As Reese follows Gen to school, several thugs pull up and grab the girl. Reese intervenes and Gen runs off. Their leader, Tremors, takes one of his men and runs after Gen, who runs into a basement stairwell. Sam steps out in front of her and opens fire, driving the two mobsters off.
A car crashes on the highway and the EMTs arrive at the scene. They confirm that the driver is DOA but the one passenger, a 10-year-old girl, is still alive but trapped in the backseat. An EMT talks to her and learns that her name is Sameen.
Sam take Gen back to the housing building while the mobsters continue their pursuit. Reese moves into the building while Gen figures that the mobsters are after her because she's a spy. While Sam argues with the girl, Reese tells Finch about the mobster in charge, Tremors, and the fact that his hands were trembling. They figure that he might have Parkinson's and Finch tries to get a positive ID, while Gen hesitantly taps Sam. When Sam responds, Gen admits that she thought that she was a robot.
Finch checks with Carter bus she isn't able to find anyone matching Tremors' description. She checks the housing project files and tells Finch that it's in a camera blind spot. As Carter talks on the phone, she's unaware that Laskey is watching her. He calls and tells Simmons that Carter is making another of her secret calls, and Simmons tells him to find out what she's up to. The young officer then gets in the car with Carter and casually asks where she was the other night. She ducks his question and notices that he has a new gun, and Laskey admits that he bought it in New Jersey and illegally brought it over state lines. Carter warns him that the law requires that he have a ballistic test on file and takes it, assuring Laskey that she'll take care of it.
Simmons calls Tremors to ask if he has the girl, and the mobster says that they'll soon capture her. He warns Simmons that the girl has backup.
While Reese makes sure that Sam's escape route is clear, Gen peppers the woman with questions. She assumes that Sam is working with some agency, and Sam insists that she's not sure what they are. Sam hears the mobsters move in and rather desperately offers to abandon Gen and go after them, but Finch tells her to get the girl out while Reese takes care of them. The kidnappers spot Sam and give chase, and Gen leads Sam to an air vent into the steam tunnels. At the center of the building is a "listening station" where Gen has set up tape recorders to listen to everyone in the building. Someone has cut the cables and Sam tells Finch that someone found out what Gen was doing, and now they want her dead. Gen explains that she was just trying to get rid of the drug dealers in the building by gathering evidence against them. She assures Sam that she has the tapes hidden and refuses to say where, but Sam convinces her that she's a fellow spy. Once she has the location, Sam relays the information to Finch.
Reese moves in as Tremors and his men find the air vent. He opens fire and the other mobsters pin him down while Tremors calls to have more of his men bring in gas masks and chemical gas. Meanwhile, Gen tells Sam that Yuri was in the KGB and taught her how to be a spy. She shows Sam the Order of Linen medal that Yuri gave her, and Sam suggests that she sell it. Gen, shocked, wonders what's wrong with her, and Sam admits that she doesn't feel emotions ever since she was Gen's age.
Gas starts pouring in through the tunnels and Sam tries to get Gen out. However, the mobsters are wearing masks and come after them. Sam takes out one but another one knocks her out and grabs Gen.
While the EMTs cut open the car, the first one talks to Sameen and tries to distract her. He asks about her home and Sameen explains that her father is in the military and they travel around a lot. They finally cut Sameen out and the EMT says that they'll call her mom as he takes the girl to the ambulance.
One of Tremors' men dumps Sam in the trunk of a car and drives her to an isolated spot to kill her. However, she has already freed herself and knocks him out with a tire iron when he opens the trunk. She calls Finch, who is on the street with Reese and Bear. The dog hasn't been able to pick up Gen's scent. Finch gives Sam the name of a doctor who owes them a favor and tells her to see him while they handle the situation, and then removes Gen's tapes from the out-of-order payphone that she hid them in. Sam wonders if Finch is punishing her, and he assures her that they're just trying to protect her. Once Finch hang sup, Sam checks the unconscious mobster and finds a familiar-looking packet of drugs.
Carter stops at a food truck and tells Laskey to get her some food. She then puts on some street clothing and heads down the street to where Tierney is paying off the driver of a chemical tanker truck. Carter takes more surveillance photos and clones Tierney's phone, listening as Simmons tells him to make the payoff. She calls Laskey and tells him to take the car back to the precinct and cover for her because something has come up.
At headquarters, Finch listens to one of Gen's tapes. When he checks Sam's GPS tracker on her cell phone, he realizes that she isn't going to the doctor. He calls her after confirming that she's back at Vadim's apartment. Once Finch admits they don't have a lead on Gen's whereabouts, Sam ignores him and breaks into the apartment. She points out that the men who abducted Gen had the same drug packets that Vadim had in his apartment, and tempts him with some of the drugs. Vadim quickly breaks and tells her that Tremors and his men regularly sweep for wires. They found out that Gen was recording them and paid Vadim to find the tapes. Once he says where Tremors is located, Sam gives him the drugs and then smashes his head through a table.
Finch locates the tape that the mobsters are after, which has Yogorov talking to Simmons. Meanwhile, Reese tracks one of the kidnapper's cell phones and runs into Carter, They watch as Tremors meets up with Tierney and collects a payment of drugs. As Tierney drives up, Reese walks up and casually punches Tremors unconscious.
Simmons goes to the manufacturing plant where Gen is tied up and tells her that it's not polite to spy on people. He asks her where the tapes are.
The EMT finally tells Sameen that her father is dead and her mother is on the way. The girl, seemingly undisturbed, asks for a sandwich.
When Finch calls Sam to tell her to get to the doctor, she throws away the phone. Reese calls in to tell him that Carter has learned that HR used Gen's fingerprints on file with the IRS to identify who taped them. Finch plays the tape, which has a conversation of Simmons telling Yogorov that the head of HR wants everyone in New York buying new bath salt drugs from HR, which is manufacturing the substance. The tanker that Tierney met with earlier contains a chemical that's a key ingredient in the drug. The drug causes tremors in people exposed to it, and they figure that Tremors is manufacturing the drugs for HR. The meeting Simmons and Tierney set up is for the HR boss to tell the other distributors that they'll be buying exclusive from HR from now on.
Reese and Carter have taken Tremors to a rooftop and Reese pours some yellow liquid into a vial and balances it on Tremors' hand, and says that it's nitroglycerine. He quickly confirms that meeting Simmons and Tierney set up is for the HR boss to tell the other distributors that they'll be buying exclusive from HR from now on. Tremors only made one batch before he was exposed to the chemical and developed his symptoms, and he doesn't know where they are manufacturing it now. Satisfied, Reese leaves with Carter. When she wonders about the nitroglycerine, Reese tells her that it's actually corn syrup. Carter agrees that they have to trade the tapes for Gen, even though it will cost her the evidence she needs to put HR away for good.
Sam goes to the building where Yogorov is and calls in an ambulance, reporting a heart attack. As the EMTs arrive and distract the men on guard, Sam sneaks into the building and captures Yogorov. She forces him to tell her where Gen is and then gives herself a transfusion of his blood to replace what she's lost because of her injury. Sam then tells him to call Simmons. Sam takes the phone and tells Gen that she's coming, and Simmons offers to deal.
Finch is trying to transfer the analog tapes so that they have a copy as evidence, but warns Reese that it will take hours to transfer everything. Sam enters the library and tells Finch that she needs the tapes to save Gen.
Once Sam leaves, Finch notifies Reese of what happened and that Sam is making the trade at Randall's Island. Reese passes the information onto Carter and says that he'll be there as well to even the odds. Laskey, who has cloned Carter's phone, listens in and calls Simmons to warn him. He then goes over and ask Carter to talk privately with him at a nearby bar because he's having a problem with someone on the job, and she agrees.
At Randall's Island, Simmons has his men take up position for an ambush. When he calls to make sure they're in place, he gets no answer. Reese steps out and demands the girl, and Simmons admits that he didn't bring her. He figures that the tapes aren't there and drops his gun, daring Reese to take him on. Reese holsters his gun and Simmons charges him.
With Finch's help, Sam tracks Tierney's signal to the chem lab where HR is manufacturing the bath salts.
Reese finally takes down Simmons, who warns that there are hundreds just like him and Reese stopping him means nothing. The police arrive and Reese quickly leaves.
Sam blasts her way past the HR men and the Russians and finds Gen, unharmed. Finch checks in and Sam asks how much he knows about chemistry. A few minutes later, Sam takes Gen out of the building, which explodes behind them.
At the bar, Carter asks what the problem is. The bartender, Jerry, gets them drinks and Laskey explains that he's having a problem with her. He admits that he knows all about her secret calls and her meetings with the man in the suit. Carter shows him a photo she's taken of Laskey with Tierney and tells him that she's known all along that she works with HR. Laskey tells her that the man in the suit is going to pay the price, but Carter tells him that they fed Laskey bad information about the meet to discredit him with Simmons. When the HR mole threatens to kill her, Carter says that she knows he's afraid of her and dares him to make a move. She also knows that Jerry is a crooked cop in vice that bought the bar with payoffs. Jerry goes for his shotgun and Carter shoots him dead, and then turns and holds Laskey at gunpoint. When he points out that she just murdered a cop, Carter reveals that she used Laskey's gun that she took from him earlier. However, she's not going to turn Laskey in because he's going to work for her now.
The EMT tells his co-workers that there must be something emotionally wrong with Sameen.
Sometime later, Sam takes Gen to her new private school and says that Finch has adopted her as a war and will make sure that she's taken care of. Gen gives her friend Yuri's Medal of Lenin and asks her not to sell it. She says that even though it may not mean anything to Sam, it means something to her that Sam has it. Sam takes it and admits that she isn't capable of emotions, but Gen assures her that they're there--just buried deep. Sam hugs her until it hurts, and then lets the girl go inside. Finch comes over and Sam wonders if she's fired because she disobeyed her orders. As they walk off, Finch assures her that she finally got the job.
That night, Sam is sleeping in her cheap apartment, the Medal of Lenin hanging from her lamp. Root comes in and tasers her unconscious, assuring Sam that they're going to have a lot of fun together.