The Machine homes in on a relevant conversation, as a man calls to inform another man that Daniel Aquino has been asking too many questions. They figure they have a solution on hand, and send someone to kill Daniel.
In Berlin, a woman, Sam Shaw, makes her way down the street and enters her apartment building. Two men confront her and talk in German, and Sam doesn't understand them. A policeman notices the confrontation but Sam says that it's just a mistake and assures him that everything is fine. The two man start speaking in Arabic, draw guns, and advance on Sam and the policeman. One of them takes out a cell phone and starts dialing. Before he can do anything, Sam draws a gun, shoots the two attackers dead, and tells the policeman in German to kneel. Once she checks her attacker's bodies, she knocks the policeman out and tells her technician, Michael Cole, via earbud that she hasn't seen Bekhti. Sam admits that she had to shoot their best chance of finding Bekhti but she did get eight numbers from the man who was dialing the phone before she had to shoot him.
Cole traces the signal and he takes Sam to the building where he traced the signal. They go to the roof and Cole lowers a microphone down into the apartment. Bekhti and his team are making a dirty bomb. Sam calls her Control and requests permission to engage. Control gives her a green light and she takes out a gun and goes downstairs.
after Cole lowers a gas line into the apartment, Sam tapes the door jamb shut. The terrorists inside pass out and Sam dons a gas mask and breaks into the apartment. She removes the cesium but then notices that the kitchen window is open. When she checks the kitchen, she discovers that one of the terrorists has revived. Bekhti attacks her and then runs off, and Sam searches the apartment. Cole finally pinpoints Bekhti hiding behind the wall to her right, and she shoots through the wall, killing him. Sam tells Cole to pull the fire alarm while she recovers her bullets so there's no trace of their presence.
Once she cleans up, Sam says that Bekhti's wiring was faulty and she fixed it. She tells Cole that she'll see him later, but he tells her that Control called and told them that they have another Number. As Sam walks away, Bekhti's apartment explodes behind her.
A day later, Sam arrives in New York City and meets with her superior, Wilson. He's unhappy that she blew up Bekhti's apartment but Sam insists it was the best way to cover their tracks. Wilson then gives her a new Number, written on a newspaper.
The next day, Sam watches the new Number, James Mercer. Cole runs a background check on the man, who was in the army, received a dishonorable discharge, and joined a militia. A week ago he received 10K from an offshore account and moved to Queens. As Sam follows Mercer she sees a good-looking man in a suit seemingly watching her. The man, Reese, walks away, while Sam listens in as Mercer gets a call saying that tomorrow is the big day.
That night, Sam equips herself in their van and notices that Cole is upset. He wonders how Research gets the Numbers and wonders if sometimes they're wrong. Cole says that the man they killed two years ago, Aquino, had no idea why he was dying. Sam points out that Aquino was selling centrifuge details to Hezbollah and Cole confirmed that the money trail led to Aquino. She insists that Research was right and that they get the Numbers from people they torture. Cole says that they were wrong that time and Sam realizes that he went behind her back. The technician explains that he had a friend in the agency check the money transfer to Aquino and confirm that it came from the U.S. government. He's requested an internal investigation from Wilson, but insists that he kept Sam out of it.
Mercer leaves his apartment and Cole and Sam break in. Cole checks his computer and immediately gets access, and finds emails from ex-military contacts. He realizes that their names are all over the file. Someone fires a gun outside and a message window comes up on Mercer's computer, telling Cole and Sam that it's a trap and they need to get out. Cole yells a warning to Sam and then dives at her, knocking her to the ground as men fire through the door. Sam takes them out and grabs one of their radios and tells Cole that they need to move. He says that he was just trying to cover her back and be her hero, and then dies.
Sam heads out, taking out the backup team. She grabs one man and shoves a flash-bang grenade into his gas mask. Reese comes out of the shadows and says that he's here to help her. She shoots him in the chest and he collapses, while a third team moves in. Sam grabs the man she injured with the grenade, dives out the window with him, and uses him as a makeshift pad to break her fall. After she shoots the man, Shaw goes out front and finds several wounded soldiers. Wilson steps out from around the corner, sees Sam, and shoots at her. She takes cover and returns fire, but by the time he moves in, he discovers that Sam has escaped. He calls the Special Council and says that they have a problem.
Wilson makes a full report to his superior over the radio. Meanwhile, Root comes in, still posing as Miss May, and makes sure the Special Council has everything he needs. She then goes to her desk and listens in as the Special Council tells Wilson that Sam has information that endangers the project. Wilson figures that Sam will need weapons and transportation, but is sure that he clipped her.
Sam steals a car and finds a drug dealer, Lewis. When he leans into the car to take her money, Sam drags him into the car and drives off. She goes to the dealer's apartment and captures his partner, Mullins. Once she has Lewis secure his partner, Sam tells Lewis to get her whatever medical supplies he has. When Mullins points out that she's gut shot, Sam promises that if she thinks she's losing consciousness, she'll shoot him first. The CTU agent removes the bullet and then tells Lewis to zip-tie himself before she passes out.
When Sam wakes up, she sees Lewis' supplier, Grishin, beating the two men up. She promises to kill him and when he says that he has her gun, Sam says that she has a backup piece. She shoots Grishin and his two men dead, tells Lewis to get out, and then grabs a beer from the refrigerator.
Hersh meets with the Special Council and tells his superior that Sam is one of the best. The Special Council figures they need to work out her game plan and Hersh says that she'll look into the Aquino situation and come after them at the same time. As Root leaves for the night, she listens in as Hersh says that he's already confirmed that Cole's CIA contact is Veronica Sinclair.
At the apartment, Sam brings up Cole's laptop and calls Veronica when she finds her phone number on the computer. Veronica insists that she can't be involved in it but Sam tells her to meet her at the Suffolk Hotel the next afternoon.
The next day, Sam calls Wilson and says that she'll only turn herself into Control. He refuses until she threatens to go public with the Aquino files, and tells him to have Control meet her at 11 that night. After setting a location, Sam goes to Veronica's apartment... where Root lives under yet another alias. Root explains that Cole sent her wire transfers that went to Aquino, and she confirmed that someone in the government electronically spoofed the transfers. The group responsible was the Intelligence Support Activity, working out of the Pentagon, and Sam says that she worked for them. Root says that the budget stretches back five years and is coded to something called Project Northern Lights. Aquino was part of it and they built a research facility, but Root has been unable to find out anyone else who worked there.
Before Sam can respond, she hears a clattering noise from the bathroom. She tells Root to stay where she is, picks up her gun, and goes to investigate. The real Veronica is tied up in the bathroom, resting in the chat. Root tasers Sam and drags her away, explaining that she interrogated Veronica but got nothing. She admits that she's a big fan of Sam and just needs the name that Aquino gave Sam before she killed the nuclear engineer. As Root cuffs Sam to a chair, she explains that the Numbers didn't come from Guantanamo. She's running out of time because Wilson and his men are looking for Veronica, and takes out a heating iron and unbuttons Sam's blouse. As she works, she tells Sam that she wants the name of Aquino's contact so she can find the facility. Sam tells Root that she enjoys pain and Root says that she does, too.
Before she can apply the iron, an alarm goes off on Root's PDA. She checks the video feed and discovers that Wilson's men are coming. She tells Sam that they'll do it again soon and slips out the side door as the agency team barges in. Once they secure the hotel room, their leader calls Wilson for instructions. He then takes out a syringe and prepares to inject her. Sam manages to free her hand, grab the leader's gun, and kill three of the four men. Reese kills the fourth man before he can shoot Sam. Sam considers shooting him but Reese points out that the leader managed to jab her with the syringe. He carefully removes it and tells Sam that he has a friend who wants to talk to her.
Reese takes Sam to the empty floor of an office building where Finch is waiting. He explains that they help people in trouble and they know that she worked as a counter-terrorist. Finch knows that she only receives SSNs and the information is never wrong, and gives Sam her own number. He admits that they were unable to save Cole because of their initial unfamiliarity with the situation. Sam wonders who they are if they're not with the program, but Finch simply says that they work for the same entity and it wanted them to help her. She points out that her employers are good at finding people and she only wants to live long enough to find Control. Finch says that she'll never succeed and that Cole began to suspect the truth about Research: that they don't exist. He asks her to stop running so they can keep up with her, and Sam tells Finch that Cole was one of the few friends she had and he deserved better. Finch warns her that she may very well make things worse and gives her his number in case she changes her mind. Sam gives it back to him and walks away.
The Special Council tells Wilson to get a team ready and end it once and for all.
Sam tracks the Special Council to a party where they agreed to meet. She realizes that he's not Control and the Special Council tells her that he's as close as she's going to get. He's surprised that she's trying to avenge her partner and Sam points out that they killed the one person she liked. As Wilson and his two aides come up behind her, Sam says that they should talk somewhere privately.
As they walk away, the Special Council explains that the program is the reason they haven't had a major attack. They can't let the public know because they'd lose the program, and they killed Aquino because no one person is as valuable as millions of Americans. Sam admits that she'd do the same thing in his place, and hands over Cole's research on the Aquino case. When the Special Council wonders why she didn't give it to Wilson, Sam points out that Wilson screwed up by treating her and Cole like a threat and issuing a kill order.
The Special Council is impressed, realizing that she didn't want revenge. Sam tells him that a good soldier wants revenge and protects the program, draws a gun, and kills Wilson. The Special Council tells the aides to let Sam go and she walks out, dumps the gun, and blends into the crowd. However, Hersh comes up behind her and injects her with poison. He apologizes and walks away, and Sam collapses to the sidewalk.
Later, Fusco and Carter are called in when the officer on the scene, Fleming, thinks that something looks suspicious about a woman dying of no apparent cause. They dismiss it as an overdose and tell Fleming to get some coffee. He reluctantly leaves and they tell Leon, posing as an EMT, to haul the body away.
The next morning, Sam wakes up in an ambulance as Bear licks her face. Outside, Leon is complaining to Reese and Finch that he never wants to see Sam again. He explains that he gave her the antidote and a sedative, but she woke up anyway and almost killed him. Leon drugged her again and drove her there. He quickly walks away as Sam comes over, and Reese offers her some water. She complains that they showed up late and Finch points out that they wanted her superiors to believe she was dead. She draws a hidden gun and tells them to hand over their phones. They do so and Finch gives her his card in case she changes her mind. She lets it drop to the ground and drives off in their ambulance.