Reese is with Jessica on a romantic holiday in Mexico. She is sad that he is going to be leaving soon. He tells her that he had quit the army in order to be with her. When they are just about to celebrate, they learn about the attacks on the World Trade Center.
Finch is working on an early prototype of The Machine that only covers New York. He tells Nathan Ingram that the next step would be to teach the Machine how to track people and sort those people according to the information.
Nathan Ingram is shocked when he finds out that Finch taught the Machine to ignore "irrelevant" crimes. After explaining that the Machine deletes the irrelevant crimes every night at midnight, Finch justifies the action, explaining that the machine was not built to save "somebody," but to save "everybody."
Reese, heading off to a new mission, runs into Jessica at the airport. He is surprised to hear that she is engaged to a man named Peter while she reminds him that he was the one who left in the first place. Reese tells her that "in the end we're all alone and no one's coming to save you." Jessica asks him to ask her to wait for him but Reese doesn't say anything, but rather, he mumbles the words after she leaves.
Reese meets Kara Stanton for the first time in Budapest, Hungary. Stanton promptly introduces Reese to their line of work by shooting two fellow agents who she believed to have betrayed them by taking bribes. She also tells him that now he would be behind enemy lines forever and that there would be no way back. Eventually, she assigns him the name Reese.
Carter is with the military in Iraq, interrogating a suspect and trying to get information about insurgent activity. She manages to reach out to the suspected terrorist and eventually convinces him to give her actionable intel. She sends him along with her team members to the secret location the suspect told her and the team eliminates the threat. When they return, she is shocked when she finds out that the informant was also killed.
Alicia Corwin and Denton Weeks visit Nathan Ingram in his office, informing him that the agent whose number Ingram gave to them earlier was found to be a traitor. They demand to know how the Machine works, but Ingram doesn't reveal anything. Later that day, Finch shows Ingram how the Machine operates; finding patterns in activities that no human would ordinarily look for. The Machine then perceives Ingram as a possible threat.
Kara Stanton, Reese, and Mark Snow are operating illegally in New York City, holding a government employee captive after he had tried to sell some software to the Chinese. When Reese receives permission to get some R&R, Stanton follows him to a bar and finds him talking with Jessica's husband Peter Arndt. She tells him that they're no longer like other people, and Reese reluctantly leaves with her before Jessica spots them.
A young Carl Elias is implied to have been living with a foster family. While being treated for wounds sustained during a fight which broke out after he was called a bastard due to his lack of a father, he asks his foster mother if she would be willing to help him research his father, but she tells him to let it go.
Elias formally meets his father Gianni Moretti at a restaurant, who promises him a place in his crime organization, so long as he remains loyal, tenacious, and capable. Later, Elias finds out that Moretti has double-crossed him and ordered his execution. Miraculously, he fights back and kills the assassins.
Reese and Kara Stanton are in Morocco interrogating a suspect, when Reese checks his phone and sees that Jessica had called him. He returns her call and a visibly distraught Jessica answers the phone. Sensing this, he tells her that he will come and get her in 24 hours. In the meantime, Mark Snow and Alicia Corwin send Reese and Stanton on a mission to Ordos, China, to retrieve a laptop. Snow advises Reese that Stanton had been compromised and tells him to kill her at the end of the mission.
In Ordos, Reese and Kara find the Laptop, along with all of the people who worked on the project, murdered. When they find a man still breathing, Stanton shoots him after she hears him mentioning the Machine. While waiting for extraction, they ponder the possible source of their intel. When Stanton signals the extraction team, Reese prepares to shoot her but backs off at the last moment. Instead, Stanton turns around and shoots him, telling him that she was told that he had been compromised. Reese realizes that they were not sent to China to steal the laptop, but to ensure that everyone who came into contact with it was dead, including them. A missile is launched on the site and Reese escapes, believing Stanton to be dead.
Jessica and Peter are arguing and Peter pushes Jessica, who falls and hits her head on the kitchen counter top. Peter, realizing that Jessica is dead, initially starts to call 911 but stops. He stages a car accident to make it appear that Jessica died in the roll-over crash.
Reese is traveling on a bus to New Rochelle and wants to visit Jessica at the hospital where she worked when he learns about her death. He turns to leave and unknowingly bumps into Finch in a wheelchair on the way out. Reese proceeds to the home of Peter Arndt, where he breaks in and starts looking at pictures and videos of Jessica. He comes to realize that Peter was abusive toward Jessica, and when Peter returns, Reese confronts him. Peter picks up a fireplace poker and Reese attacks him.
Nathan Ingram and Alicia Corwin sit at a restaurant. Nathan tells Alicia that a freight train will secretly transport The Machine to its new location. Alicia ensures him that the new location will be safe and that the numbers, when sent to the government, will be untraceable. Nathan says that they need to make sure nobody, apart from the eight who already know about it, can ever know about the machine. Alicia corrects him, saying that only seven people know about, barring anybody he told. Nathan shrugs it off as a simple arithmetic error.
Finch and Ingram prepare the Machine for shipment to its new home. After meeting with Alicia Corwin, Ingram is worried that the Machine might end up in the wrong hands and suggests that they build a backdoor. Finch, however, prefers to trust the Machine as built and warns Ingram that every exploit is a total exploit. Without telling Finch, Ingram secretly installs a contingency.