Samantha Groves and Hanna Frey are playing computer games in the library in their hometown Bishop, TX, but Hanna always loses. When the library closes, Sam sees her friend getting into a car, thus making her a witness to Hanna's disappearance. Unbeknownst to Hanna, Sam successfully finishes the game just after she leaves and enters Root as her username.
Finch and Nathan are walking in the park. Nathan is unhappy about their relationship and asks about their little project. Finch explains that he had taught the Machine to understand people and find connections between them when it detects an anomaly and points Finch to a woman named Grace Hendricks, who is painting at the railing. Finch assumes that it's a bug because there seems to be no reason for the Machine to select her.
Finch tests the Machine's ability to find connections between random people when it shows him information about Grace Hendricks, the painter. Finch suspects that the bug still exists when he learns that she likes Charles Dickens and that there is also not a single anomaly in her life, which makes her different from other people.
On Grace's birthday, she receives a letter from a bike messenger informing her that Finch has created for her a birthday scavenger hunt. She tours around the city, eventually ending up at the Guggenheim Museum, where Finch is waiting for her. Together, they tour the museum, and Finch begins to tell her something that he thinks she needs to know, but she stops him, and the two kiss.
Finch meets Nathan for dinner, where Nathan deduces that Finch is seeing someone. He tells Finch that a little mystery goes a long way and that he has just returned from his friend's wedding, during which he saw his ex-wife Olivia. Nathan explains that he's told her so many lies over the years that he doesn't even remember what happened any more.
In Prague, Reese and Kara enter a hotel room where three men are concluding a deal involving combat drones. Reese and Kara pose as hotel guests, then Reese kills two men and Kara kills the other. Reese is visibly nervous and Kara has to calm him, explaining that the people that they killed were enemy combatants and that killing people is in fact their job. And in order for Reese to be good at his job, he'll have to learn to love it.
In Paris, Reese and Kara sit at a bar discussing the next group of people they are supposed to kill. Reese questions the fact that the people are bad, and Kara says that orders are orders. She tells him that he needs to decide whether he's cut out for his job or not, to which John replies that he loves his job. The partners kiss afterward.
Reese has just received orders from Mark Snow to "retire" Agent Stanton after their mission in Ordos. (“Matsya Nyaya”) As he leaves the room, Stanton notices a worried look on Reese's face and tells him to shut it down, because she "needs the killer", not the Boy Scout.
When Kara Stanton and Reese find out they have been double crossed during their mission at Ordos(“Matsya Nyaya”), they run for their lives. Kara survives and regains consciousness some time later, finding several men holding her at gunpoint. She is then taken to hospital in Dongsheng, where she is greeted by a man who had been following her CIA activities and knows almost everything about her.
Using the tale of the mythical Titans as an analogy, Greer offers Kara answers about why the government wanted her dead. He then tells her that if she will assist him in dispersing a virus, he will tell her who sold the Laptop that Reese and Kara were sent to Ordos to destroy, the man responsible for all that happened to her.
Finch is working at IFT Plaza when Nathan Ingram turns on the TV. They listen as the news covers the events of 9/11. They say that they started IFT to change the world, and they grew wealthier and wealthier, but failed to meet their goal. 9/11, however, changed the world. They say that they need to change the world before someone else does.
Nathan tells Finch that The Machine was their chance and expresses disappointment in Finch's giving it away. Nathan asks Finch what would happen if they built a backdoor into the machine, but Finch wants to hear nothing of it. He tells Nathan that they either move on to their next venture together, or they don't. Nathan then walks out the door without saying a word.
Nathan holds up the social security number and a photo of a woman and is watching her from his car. When she leaves her house, Nathan sees a man following her and pulls out a gun, preparing to intervene.
Fusco sits at a bar and asks the bartender for another drink. His partner, Detective Stills, tells him he's had enough and should go home. Fusco tells Stills that he can't go home because his wife has kicked him out of the house. Stills asks Fusco to stay the night at his house.
Fusco knocks on a door and Stills opens it. He lets Fusco in and Fusco sees that Stills and Azarello have killed a man in what they claim is self-defense. They ask Fusco to cover for them, and they guilt him into doing so.
Fusco enters an apartment where Stills and Azarello have killed several people. Once again, they ask Fusco to cover for them and he refuses this time. A man jumps out of an armoire, and Fusco shoots him in self-defense. He is forced to cover for his partners as a result.
Finch goes over to Nathan Ingram's house and they reminisce about their past adventures and discuss current ones. Harold tells Nathan that he plans to propose to Grace and as a result, he'll have to tell her the truth about his background. Suddenly Nathan's phone buzzes and shows a new irrelevant number.
Finch follows Nathan Ingram into the Library, and Finch asks what it is. Nathan proposes that Finch thinks of him as a liability. Finch sees photos on a board, and realizes that Nathan had installed a backdoor into the Machine. Nathan explains that the Machine "was waiting" for him, and that he took precautions. Finch tells him that the precautions would be essentially worthless and threatens to put a stop to Nathan's side operation. Finch tells Nathan that they can't save everyone and shuts down the irrelevant section of the Machine, just as Nathan's number comes up.
Hersh is in an interrogation room with a man suspected of attempting to bomb a ferry, Asif, and a translator. The man says he was attempting to load semtex onto a van next to the Liberty Island ferry and that he would be the detonator. Hersh shoots the translator and sticks the suspected terrorist with a needle, making him go limp.
Finch and Nathan Ingram meet at The Library, and Nathan tells Finch that he plans to meet with a reporter and tell her about the work he and Finch have done. Finch says that Nathan shouldn't do that and hypothesizes that Hersh is killing the relevants. Finch warns Nathan that calling a journalist will put their lives at risk.
Finch follows Nathan to the place where he plans on meeting the reporter. Watching Nathan through the windshield of a van, Hersh wakes up Asif and shows him the explosives packed into the van. He tells Asif that he has completed his mission and leaves. Nathan spots Finch, and an explosion is seen and heard behind Nathan.
Finch wakes up at a facility where victims of the terrorist attack at the Ferry are being held, and a doctor tells him that he has sustained injuries to his neck and lower back. He frantically tries to find Nathan and eventually finds him, dead. He gets up out of bed on his own and hides behind a wall as Grace looks for him. Grace asks one of the guards where Finch is, and they tell her that if she doesn't see him, he probably didn't survive. Grace finds the book that Finch placed the engagement ring into, and cries, assuming that Finch had been killed in the attack.
Finch goes back to the Library, sees that Nathan's number had come up on the irrelevant list, and re-installs the contingency. The clock then strikes midnight and Nathan's number is erased from the system.