Carter wakes up in the wreckage of Donnelly's SUV, still handcuffed. Finch calls her and Carter tells him what happened. Once she finds the key for the handcuffs in Donnelly's pocket, Carter frees herself and tells Finch that nobody saw her with Reese and Donnelly. As sirens sound in the distance, Carter leaves the crime scene and tells Finch that Kara was the woman who attacked them and abducted Reese. Finch says that he knows what Kara wants and looks pensively at a file on the ex-CIA assassin.
The next morning, Reese wakes up and finds himself looking at Kara. He and Snow are seated on a bus and Kara is across the aisle. Kara reminds them that Snow secretly ordered her and Reese to kill each other, while Reese discovers there's a bomb vest wired to his chest. She demonstrates how she can arm it using her cell phone and explains that she wants Reese to understand that he can't fight her. When Reese asks what she wants, Kara tell him that they're going on one last mission together, just like the old days. She gives Reese an earbud and a list and tells the two men that if they complete her mission then they'll live. Kara kicks a bag full of guns to them and says that the mission concerns what they'll do now that they no longer work for the CIA.
Carter goes home to bandage her injuries and Finch calls. He tells her that Donnelly was found dead in a car wreck and the FBI want her there because she worked with Donnelly. When Carter arrives, Fusco explains what happened and asks if she's heard from Reese or Finch. He notices that she's missing an earring and Carter claims it must have fell off. SAIC Moss comes over and asks Carter when she last saw Donnelly. She claims it was at Rikers and Moss admits that the FBI thought that Donnelly was paranoid about the man in the suit and his supposed government contacts.
Once Moss leaves, Carter goes to the wreckage to find the incriminating earring. Fusco comes over and gives it to her, and asks what's going on. Carter admits that she doesn't know but suggests that they talk to the person who does. They soon set up a meeting with Finch, who says that he hasn't been able to find much about Kara's time with the CIA. Carter confirms that Kara had Snow steal a high-capacity hard drive from the tech company where she saw him, and Finch has her tell him everything she knows about the theft.
Reese and Snow go to a basement apartment and meet with an underground tech, Petar. He and his friend are playing a first-person shooter and Kara tells Reese to get the hard drive from them. Peter demands another $50,000 and Kara tells Reese to break his neck. When Reese tries to negotiate, Petar refuses and Kara arms the vest. Before Petar and his men can kill the two ex-agent, Kara shoots the two killers dead from a window across the street. As Reese picks up the hard drive, Kara tells him that 's his only warning.
After the bombing on Ordos, an injured Kara wakes up surrounded by Chinese soldiers. She's taken to a hospital to recover an Englishman, Greer, comes in to visit her. He says that already knows almost everything about her and shows her the laptop that her superiors sent her to recover. He says that it's the answer to an interesting question and asks Kara if she wants to know what the question is. Kara dismissively says that she doesn't care and Greer assures her that they'll get along fine.
Kara takes Snow and Reese to a diner, and Snow digs in while Reese refuses to eat. His former partner says that she's well aware that he's trying to fight back in little ways while he tries to figure out a way to get around the bomb vest, and Reese tells her that she'll know when he fights back. Snow, amused, listens to the exchange and says that he was right to order them to kill each other at Ordos, considering it poetic justice. Two men go outside and Kara tells Reese and Snow to follow them and steal their car. The two men knock out the customers and Snow strangles his opponent until Reese pulls him off. Reese confirms that the two men are ATF agents and Kara tells them to put on the agents' jackets. When one agent's cell phone rings, Kara tells Reese to answer it. The agents' superior tells Reese that they have a situation and provides an address, and Kara tells Reese and Snow to take the jackets and throw away their cell phones.
Finch is at headquarters when Carter calls to tell him that the hard drive that Snow stole was a from an exclusive NSA-certified batch made for military installations. Finch figures that Kara is using it to store something that she plans to steal. Reese sends a text message to Finch with the letters UXO, and Carter explains that the letters are military code for unexploded ordinance. Finch traces the GPS location of the phone and sends Carter and Fusco to investigate.
When Reese and Snow arrive, they discover that the police and the ATF are evacuating the office building because of a bomb threat. Kara tells them over the earpieces that she called in the threat and orders them to go in. Reese intimidates the officer on duty into letting them in and they take the elevator up.
Carter and Fusco trace Reese's phone to the diner and find the unconscious ATF agents. When they learn that the ATF has been summoned to the office building, Finch confirms that the building has an unlisted floor occupied by a shell company. He figures that whatever is there, Kara plans to steal.
As Reese sprays over the security cameras, Kara gives him the access code to the 21st floor and explains that there is a level 5 DOD facility there. Snow and Reese take out the two Delta Force operatives on guard and tie them up. When one of them hits Snow, he prepares to shoot the man dead but Reese intervenes. Kara warns them that the floor's electronic shielding may cause signal interference so she arms their bomb vests to detonate in 15 minutes.
As Kara continues to recuperate in the Chinese hospital, Greer visits her and explains that he doesn't work for the Chinese government as she believes. Rather than explain who he does work for, Greer tells Kara that the CIA betrayed her because they know what will happen next and are afraid. Greer's people believe that Kara can be useful to them, and he tells her that he can offer her an answer to any question. Kara hesitates and then asks who gave the order for her death. Greer tells her that the person responsible was also the one who sold the laptop to the Chinese.
Reese and Snow reach the floor's security desk and erase the last two hours of camera video. Kara then tells them to find a technician in a nearby temperature-controlled research room.
Fusco and Carter arrive downstairs and Finch goes to Times Squares to hack the DoD computer from a location where he can't be traced. He then calls the detectives and tells them that the DoD installation is conducting research into cyber-warfare viruses. Finch figures that Kara has sent Reese and Snow in to steal a virus and then use it to shut down computers across the U.S. After flashing their badges to get inside, Carter tells Fusco that they have to take the stairs.
Snow and Reese find an electronics lab, but Kara refuses to tell them what they're looking for. A technician, Kevin, comes out and Reese grabs him. They take out the guard and then use Kevin's palm print to open the secure door. As they start downloading the virus, Reese realizes that the lab walls have cut off Kara's signal. Now that she can't listen in, he tells Snow that they have to do something. The former CIA agent refuses, saying they don't have enough time, and tells Reese to find the servers. As Kevin leads Reese away, Reese tells the technician that he'll keep him alive.
Once he's away from Snow, Reese calls Finch, who explains what Kara wants. Kevin confirms that the DoD computers aren't networked to any outside system, while Finch realizes that Kara is looking for a new virus, codename Cygnus, that can shut down any and all computers... including The Machine. Reese tells Finch to get clear of the building before his vest explodes and then asks Kevin if he can wipe the system. The technician explains that the only way to do it is to cause a security breach in the system.
Reese removes a drive from the computer, causing a breach and activating the system wipe. Snow realizes what Reese is doing and attacks him, but Reese defends himself. Kara walks in and activates their vests. She knew that Reese wouldn't follow orders and accuses him of losing his nerve. When Reese tells her that she's too late, Kara says that her whole plan was for them to clear a path so she could inside. They go into the next room and Kara puts the stolen drive into the computers. Kevin realizes that she plans to upload a virus into the system, and from there across the U.S. Reese tells his ex-partner that it isn't too late to end it and she can still change her mind, but Kara simply smiles and strokes his cheek. She then resets the bomb vests for five minutes, walks out, and seals the door behind her.
Reese tells Kevin to get the door open and the technician overloads the power supply, setting off an emergency shutdown. When the emergency batteries kick in, Reese and Snow shoot them out, unlocking the door. They leave and Reese tells Snow that they have to get to the roof so the bombs will detonate without killing anyone else. Snow knocks him down from behind and says that he'll take his chances at a CIA safehouse two blocks away. Reese warns the man that the CIA will execute Snow because he's been compromised, but Snow wishes Reese luck and leaves.
Fusco and Carter arrive and Carter offers to defuse the bomb. Reese reminds her that she has a son and that she can't afford to risk her life. Fusco agrees and Carter insists that Reese doesn't have to sacrifice his life, but he says that he does... and that she'd do the same thing in his place. He thanks them both and Fusco leads his partner away.
When Reese goes to the roof, he finds Finch waiting for him. He gives his partner the drive and tells him the virus that Kara has released, and then draws a gun on Finch. However, when Reese realizes that Finch won't abandon him, he lowers the gun. Finch goes to work and confirms that the bomb is triggered by a cell phone signal. As two minutes count down, Finch prepares to hack the phone's unlock code, explaining that there are five possible numbers. However, the phone will lock them out automatically after three attempts. Finch tries one number and fails.
Carter and Fusco wait on the street and watch.
Finch tries a second number and it also fails.
Kara calls Greer and tells him that the virus has been planted. She demands to know who betrayed her and Greer says that all he has is a name. The person responsible doesn't exist in any known database. Greer gives her the number and Kara writes it down on a piece of paper.
As Finch prepares to enter the third and final number, Reese reminds Finch of how he said they'd probably both die, when they first met. He admits that he would have been dead already if Finch hadn't found him and given him a job, and then tells his friend to pick a winner. Finch enters a third number... and then changes his mind and enters a different one instead.
Kara gets into her car and takes her cell phone out.
Finch enters the last number and the phone unlocks. He disarms the bomb signal and shares a sigh of relief with Reese.
Kara spins around when Snow speaks up from the back seat of her car. He says that she was right and that he'd be good at dying. Desperate, Kara lunges at him over the seat.
Carter and Finch realize that Reese and Finch are safe. Kara's car explodes down the street. As they run to it, Reese realizes that Snow sacrificed himself to stop Kara.
The next morning, Finch is already working when Reese comes into their headquarters. Bear runs to his master and practically bowls him over.
Carter is working at the station when Moss comes in and tells her that they've confirmed that Kara and Snow were the two suicide bombers. The FBI has photos on Snow and figure that he was the man in the suit, and they're closing the case now that he's dead. Moss tells Carter that he'll take care of Donnelly and Donnelly leaves. Once he's gone, Fusco comes over and asks if they're okay, and Carter says that they'll soon find out.
As Reese looks at a photo of Kara, Finch checks the malware that she planted and tells Reese that it is set to trigger in five months. Reese thanks Finch for saving his life and his friend says not to mention it.
The Machine reviews the security tapes of the explosion. As the car explodes, a piece of paper is blown clear. It flutters down to the street... and has the name "Harold Finch" on it.