Two years earlier, The Machine picks up a conversation as two men agree by phone to eliminate nuclear engineer Daniel Aquino. They send someone to kill Aquino and The Machine watches as a killer disposes of Aquino, who has no understanding of why he's being murdered.
In Berlin, Sam Shaw enters an apartment building and two men confront her. They initially give her orders in German but Sam doesn't seem to understand. A local police officer notes the meeting and tries to intervene, and the two men draw guns and bark orders in Arabic. One of them takes out a cell phone and stars dialing, and Sam draws a gun and shoots them both dead. She then knocks out the policeman and contacts her technician and field support officer, Michael Cole, via her earbud. Sam informs Cole that she hasn't seen Bekhti but she did get the first eight numbers of hi cell phone from the man who was dialing the phone.
Cole traces the numbers and he and Sam go to the building where the call went. They go to the roof and lower a microphone/camera down the ventilator shaft into Bekhti's apartment, and watch as the terrorists and his comrades assemble a "dirty" cesium bomb. Sam contacts her Control and gets permission to take Bekhti and his men out.
While Cole pumps knockout gas into the apartment, Sam dons a gas mask and breaks in. As she recovers the cesium, she notices that the kitchen window is open. Bekhti, lying closes to the window, recovers consciousness and attacks her. When Sam gets the upper hand, he ducks away and hides in the apartment. Using the camera, Cole spots Bekhti preparing to ambush his partner. When he warns her, Sam shoots through the wall, killing the terrorist. She then tells Cole to trigger the fire alarm while she cleans up the crime scene. Once she's done, Sam goes to the street and tells Cole that she'll see him later. However, Cole tells her that they've received a new Number from Research and that they'll be heading to New York City. As Sam walks down the street, the explosive she rigged in Bekhti's apartment goes off.
A day later, Sam and Cole arrive in New York and Sam meets with her immediate superior, Wilson. He jokingly complains about her blowing up the apartment but Sam insists that it was necessary. Wilson then gives her the newest Number. Sam begins tailing the man, James Mercer, while Cole confirms that the man was a former U.S. soldier who was given a dishonorable discharge and joined a militia group. Someone paid Mercer $10,000 through an offshore account to move to Queens and wait for orders. As Sam follows Mercer, she notices a man--Reese--looking at her. She assumes that she's been made but Reese walks off and Sam tells Coe that everything is fine. The two CTU agents monitor Mercer's cell phone and hear him receive a message saying that tomorrow is the big day.
That night, Sam returns to Cole's surveillance van to prepare to break into Mercer's apartment. He appears uncertain and finally asks if she wonders how Research gets the numbers and if they're ever wrong. He reminds her of one target, Aquino, who seemed to have no idea why he deserved death. Sam figures that Research is torturing prisoners in Guantanamo to get the information, and reminds her partner that he was the one who confirmed the wire transfers from Hezabollah to Aquino in return for details on centrifuges. Undeterred, Cole says that he contacted a friend in the CIA and she confirmed that the spoofed money transfer actually came from the U.S. government. Sam realizes that her partner has done something stupid and Cole admits that he asked Wilson for an internal investigation. However, he promises to keep Sam out of it.
Once Mercer leaves his apartment, Cole and Sam break in and check his laptop computer. Cole is surprised to discover that it isn't password-protect and he brings up Mercer's emails... and realizes that he and Sam are named in the emails. As gunshots break out on the sidewalk, a message window comes up telling the partners that it's a trap. As Sam checks the windows, Cole catches a glimpse of moving figures on the other side of the door and tackles Sam just as they fire. A tactical agent breaks in and Sam takes him out and steals his radio, and then goes to Cole. She realizes that he's mortally wounded and Cole say that he just wanted to be her hero once... and then dies.
Sam leaves Mercer's apartment and takes out the second team of tac agents, grabbing one of them and shoving a flash-bang grenade into his gas mask. As it goes off, Reese steps out of the shadows and tells Sam that he's there to help her. She shoots him in the chest and he falls back, and then grabs the downed man with the grenade and jumps out the second-story window, using his body to break her fall. Once Sam shoots him, she heads to Cole's van and discovers several knee-capped tac agents on the sidewalk. Wilson steps out, giving orders to his men, sees Sam and opens fire. She manages to escape, taking Cole's laptop with her, and Wilson calls the Special Council and says that they have a problem.
In Washington, the Special Council listens to Wilson's report, unaware that his secretary, Miss May, is actually Root. She listens in as the Special Council reminds Wilson that Sam has dangerous knowledge of the project and must be eliminated. Wilson assures his superior that he wounded Sam and that she'll have to go to ground to get weapons and transportation.
After stealing a car, Sam approaches a drug dealer. Lewis. When he gets close enough, Sam drags him into the car and drives away. Once she gets his address, she goes there and gets the drop on Lewis' partner, Mullins. Sam has Lewis zip-tie Mullins to the radiator and then has him get a knife, thread, and towels. She then removes the bullet from her side, promising the two men that if she passes out then she'll kill them first. As she works, Lewis points out that she knows medicine and Sam admits that she took a medical degree before joining the Marines. Once she removes the bullet, Sam has Lewis zip-tie himself to the radiator as well before she passes out from shock.
When Sam wakes up, it's to Lewis' supplier, Grishin, beating up Lewis and Mullins. Grishin has Sam's gun and asks why she's there, and she promises to kill him. When he points out that she has her gun, Sam draws a backup and shoots Grishin and his men. She then frees Lewis, tells him to get out, and drinks a beer from the drug dealer's refrigerator.
The Special Council calls in Hersh, who warns him that Sam is the best soldier they have. When the Special Council wonders whether she'll come after them or investigate Aquino's death, Hersh warns him that she'll do both. Outside, Root listens in as Hersh tells the Special Council that they've confirmed that Cole's CIA contact is Veronica Sinclair.
At Lewis' apartment, Sam checks Cole's laptop and finds Veronica's phone number. When she calls the CIA contact, Veronica refuses to help at first but Sam warns her that she can help her or die. The CIA woman agrees to meet Sam at the Suffolk Hotel the next afternoon.
The next day, Sam calls Wilson on a disposable phone and agrees to turn herself in, but only to Control. If Wilson doesn't arrange the meeting, Sam says that she'll go public with the Aquino files. Wilson reluctantly agrees and Sam tells him that she'll find Control at 11 that night. She then goes to meet with Veronica... unaware that it's Root. Root lets her into the hotel room and explains that she helped Cole confirm that the U.S. government spoofed the wire transfers to Aquino to make it look like he was working with terrorists. She tells Sam that the people responsible are the Intelligence Support Activity group, and Sam says that she worked with them until they tried to kill her. Root explains that the group has existed for five years and is coded under Project Northern Lights. Aquino helped build a research facility for them, but he's the only one involved with the project that Root has identified.
As Sam takes it all in, she hears someone moving in the hotel bathroom. She goes in to investigate and finds the real Victoria, bound and gagged in the tub. Root tasers Sam from behind, drags her to a chair, and zip-ties her down. She then tells the CTU agent that Victoria couldn't tell her the name that Aquino gave Sam right before she killed him. As Root plugs in an ironing dryer, she tells Sam that the Numbers she's received didn't come from Guantanamo, but from something else. She then tells Sam to give her the name or she'll proceed to torture. When Sam says that she enjoys pain, Root smiles and says that she does, too.
Root's PDA alarm goes off and she confirms that an agency tac team is heading for the hotel room. She tells Sam that she'll meet again and leaves via the adjoining room's door as the team breaks in and secures the hotel room. Their leader gets orders from Wilson to kill Sam and prepares to give her a lethal injection. As he leans over her, Sam frees one hand, grabs the leader's gun, and shoots him and three of his four man. As she tries to free herself, a fourth man prepares to shoot her... and Reese knocks him out from behind. When Sam decides whether to kill Reese as well, he points out that the leader managed to plant the syringe in Sam's shoulder before he died. She lets Reese remove it and as he works, he says that if he bumps the syringe then he'll have five minutes to administer atropine to negate the poison. Once she's free, Reese tells Sam that he has a friend who wants to talk to her.
Reese takes Sam to the empty floor of an office building to meet with Finch, who tells Sam that they help people in trouble. He knows what Sam has been doing and how she has been receiving Social Security numbers of terrorists, and then gives Sam his own Number. Finch explains that he received her Number and Cole's but were unable to intervene in time to save her partner. When Sam wonders who they work for, Finch simply says that they work for the same entity and it sent them to help her. Sam insists that she only wants to find Control and avenge her partner, but Finch warns her that she'll never succeed. Cole had to die because he realized the truth: Research doesn't exist. Finch asks Sam to stop running so they can keep up and protect her, but Sam insists on avenging Cole, one of the few friends that she ever had. Disappointed, Finch warns the CTU operative that she may make things worse and gives her his card so she can contact him if she changes her mind. Sam gives it back and leaves.
The Special Council calls to tell Wilson to get a team together and finish Sam off for good.
Later, Sam tracks the Special Council to the party that he's attending. They talk quietly and Sam realizes that the Special Council isn't Control. He informs her that he's as close as she'll ever get to Control, and is surprised that she's trying to avenge Cole given her psychological disassociation. Sam points out that they killed the one person that she liked, and she plans to get revenge. Wilson and his assistant arrive and the Sam says that they should talk privately.
Sam and the Special Council go to an isolated hallway and the Special Council explains that they've managed to avoid a major terrorist attack because of the program. However, if the public knew what they were doing, they'd end the program. The Special Council insists that Aquino's death was necessary to protect the lives of millions, and is surprised when Sam agrees with him. She hands him Cole's file on the Aquino case and explains that she wanted to give it to him directly because Wilson screwed up. She points out that rather than come to her and Cole, Wilson immediately issued a kill order.
The Special Council, impressed, realizes that Sam was carrying out her duty all along and didn't want revenge. Sam tells him that a good soldier does both, draws her gun, and kills Wilson. Realizing that she's eliminated a threat to the program, the Special Council tells Wilson's assistant to let her go. Outside, Sam dumps the gun and walks down the street... and Hersh injects her with a syringe of poison. He apologizes, admitting that she's a good soldier, and then slips away as Sam collapses to the sidewalk.
A few minutes later, Fusco and Carter arrive on the scene when a beat cop, Fleming, calls in the mysterious death. He points out that Sam is young and appears to be in good health, and apparently died of no apparent cause. The detectives tell him that it's probably an overdose and advise him to get some coffee. Once Fleming leaves, Leon arrives, posing as an EMT, and helps Fusco carry Sam's body into an ambulance.
The next morning, Sam wakes up to find Bear licking her face. She gets out of the ambulance and finds herself in a cemetery. Leon is complaining to Reese and Finch that he doesn't get paid enough, and that Sam attacked him after he gave her the antidote. He had to give her a second sedative to get her to the cemetery. Leon quickly leaves as Sam comes over, and Finch explains that they had to cut it close so that her superiors would believe the assassination attempt had succeeded. Unconvinced, Sam draws a hidden gun on them and takes their phones. As they do, Finch gives her his card again but she drops it and steals their ambulance.