Peter Brandt is visiting his older brother Jesse and his son Frankie. As they eat, Peter says that his brother getting partial custody is doing him good, and Jesse is happy that Frankie doesn't have to hear his parents yell at each other. Peter points out that he's dry after two years, and Jesse is glad to help Peter go to law school. The doorbell rings and Jesse goes to answer it. Two FBI agents inform him that he's under arrest on a national security warrant, and refuse to tell Peter the charges. They lead Jesse away and Peter promises to get it sorted out.
The Machine is unable to analyze a threat and searches for the system admin. It's unable to locate Finch, and calculates his odds of survival as less than 30%. It then begins looking for other assets.
Reese and Sam chase a Decima man, Otto, to the roof of a building. They say that he just needs to talk to them, but he throws himself over the edge and falls to his death. Root arrives and explains that all of Decima's people have large insurance policies that go to their next of kin if they suffer an "accidental" death. If they get caught, they get nothing. Sam points out that Otto was their last lead to Finch, and Root tells them that the Machine says they have other things to worry about. She tells them that the Machine believes that Finch is safe for the moment and they have a larger threat. The Machine can't see the whole picture, so they'll be its eyes and ears.
In the empty office building, Greer tells Finch that it's a pleasure to meet him at last. Finch wonders what he wants, and Greer says that he wants to talk about the future with the father of artificial intelligence. When Finch says that it was an unintended side effect, Greer figures that he did it to experience the power of creation. Finch warns him that bringing Samaritan online is a mistake, and Greer congratulates him on playing everyone well until now... when the Machine has disappeared. He insists that the world needs structure and Samaritan will provide it, but Finch asks why he sought him out if he's confident Samaritan is under his control. Greer wants Finch with him because he's the only man who can destroy Samaritan. Once Samaritan goes fully online, the world will no longer need Finch.
Root goes to Otto's body and takes his car keys, and then goes over to his car and removes the GPS transponder so her hackers can trace the data. She leads Sam and Reese over to a nearby van where Daizo, Jason Greenfield, and Daniel Casey are waiting. Root explains that they've been on the road collecting contraband in the tri-cities, and she wants to use the team's safehouse. Reese agrees and goes up to the cab, while Root gives Sam a satphone and tells her to go to the Carlton Hotel and wait for further instructions.
Greer meets with Senator Garrison and tells him to use the beta test results to convince them to provide Samaritan with the NSA feeds. When Garrison says that they're willing to buy Samaritan, Greer says that Decima will maintain control of it and provide the government with the critical information. The senator balks at giving them the feeds just to have Decima sell the information back, but Greer assures him that Samaritan will give them all of the information as quickly and cleanly as possible. In return, the government gets plausible deniability and Decima can shoulder the blame if there is a civil liberty scandal. Greer asks if Garrison wants to let the U.S. crumble or agree to his terms, and walks away.
The hackers set up the seven stolen Samaritan servers at the safehouse, and Daizo says that they'll be ready in a couple of hours. Reese offers to help them, but Root says that she needs him for something else.
Sam arrives at the hotel and contacts Root, who has her describe what she sees. Looking around, Sam spots Secret Service agents outside and the Machine confirms that Garrison is present. It then calls Reese on a pay phone and gives him five Numbers. Meanwhile, Control leaves the hotel and Root figures that she's covering her tracks because she knows how the Machine works, and it must be something bad.
Root and Reese go to a coffee house and Root directs Sam to a room on the 15th floor. A Secret Service agent comes out and she knocks him out, and kneecaps another as he comes out. They are monitoring a separate room where Garrison and Control are meeting, and Garrison is the second Number the Machine gave Reese. In the room, Control can't believe that Garrison wants her to help Greer. The senator wants her to help them get the NSA feeds and wants her to get Rivera on board. Garrison asks her to convince Rivera of the program's special merits and gives her the beta test results as evidence. When Control wonders what she gets, Garrison explains that she'll get an open system with plausible deniability. Control asks to see the intel first.
Sam, listening in, wants to kill them immediately. Root points out that they don't know if Garrison and Control are the victims or perpetrators yet. She has Sam check the front door monitor and Root tells her that two more Numbers have arrived: General Kyle Holcombe with the NSA; and Manual Rivera, the senior adviser to the President. She hasn't identified the third Number yet. Meanwhile, a man comes in and Root asks Reese if he's ready to have some fun. When he wonders who the man is, Root admits that she has no idea.
Greer accuses Finch of hobbling the Machine, and Finch explains that the Machine developed abilities he didn't anticipate at an exponential rate. He worried that it would be too late to stop it because he couldn't anticipate its evolution. Finch worried that the Machine might determine that humanity is irrelevant, and begs Greer not to let Samaritan go online. Greer says that he plans to celebrate Samaritan's brilliance, not muzzle it, and says that he has no intention of controlling it.
Rivera and Holcombe meet with Garrison and Control, and Rivera warns that the President isn't going to risk the scandal of another surveillance program. He points out that he's been running interference on the Northern Lights debacle, and Control insists that they have to protect their country. Rivera refuses to back their plan, but Control describes his children's school and tells him that a year ago Northern Lights prevented a terrorist attack in the area of the school. Rivera says that he would have heard of it, but Control says that they couldn't advertise their activities, and that people can object because they protect them. She hands Rivera the intel on Vigilance and admits that they don't know who they're targeting next, but they have a big plan set up in 24 hours. To stop them, they need Samaritan online. Rivera agrees to read the file and Garrison says that he has a meeting across town.
Sam tells Root what Control is doing and asks if she can kill her, but Root tells her to wait. She then goes over to the man with Reese and says that they have a few questions for him. The man grabs a submachine gun from his backpack and opens fire, and Reese takes him down. They check his ID and confirm that his name is Niall Jacobs, and Niall figures that they're Federal agents. Reese finds a flash drive on him and Root checks it, and confirms that it's a self-replicating worm virus. It's designed to target a proprietary micro-switcher, but the Machine doesn't know the specific target. They figure that Niall is with Vigilance, just as Sam spots Collier and his men approaching the hotel. Root questions Niall, who says that he only knows his part and they're too late to stop the revolution from happening.
The Machine reviews Collier's record.
In Michigan, Peter meets with the prosecuting AUSA, Langdon, and tries to convince him he has the wrong guy. Langdon explains that Jesse has connections to Aziz Al-Ibrahim, whose cousin is a member of a Muslim terrorist group. The AUSA has several photos of Jesse meeting with Aziz, and two years ago Jesse turned his life around. Langdon suggests that Jesse hit bottom and asked the wrong people for help. Peter doesn't believe it but Langdon insists that surveillance doesn't lie.
After calling in Fusco to arrest Niall, Root takes Reese on another errand. She warns that both Decima and Vigilance are aware of the Machine and taking steps to blind it, and Reese tells her to get the hackers working so they can find Finch. She calls her team and they tell her they're having issues and need two hours. Daizo's working on the geo-locator data but doesn't have anything yet. After Root hangs up, she tells Reese that the hackers are working on something to slow down their enemies.
Collier and his people get in the hotel elevator and one of the team, Madison, says that she has what they need.
That night, Root tells Sam to talk to Control, and Reese reminds her that they need her alive so she can lead them to Greer and then Finch. Sam breaks in and kneecaps Control's bodyguard, and Control tells Rivera that Sam is the agent who took out the terrorist threatening his children's school. Control wonders what she wants and Sam says that she's there to rescue her.
Jason and Daniel call Root and tell her that the virus is designed to target micro-switches at the power company. Realizing what that means, Root tells Reese to help Sam and takes off on her own.
Control realizes that Sam received their Numbers, and Sam admits that she doesn't know why she's there to protect her. Reese calls to say that he's on his way... just as the power goes out throughout the city.
Jesse kills himself in jail. After the funeral, Peter is at home with his nephew and Jesse's ex-wife Shari. She wonders how they can put someone in jail without telling them why they're charged, and blames herself for taking full custody. Peter says that Jesse was drinking and they're all responsible for their own actions. Aziz comes in to offer Peter his condolences, and explains that he was Jesse's friend. When Peter wonders why he doesn't know him, Aziz shows an AA chip, and says that Jesse was his sponsor and saved his life. A distant relative caused problems for his family and he was out of the country dealing with them recently. When Peter tries to give the chip back, Aziz tells him to keep it as a reminder that Jesse saved someone's life.
As panic spreads through the city, Reese makes his way to the hotel. With the cell towers out, he's unable to call Sam.
At the office building, Greer looks out at the blacked-out city and remembers his time as a child during the Blitz. Finch has deduced that Greer joined MI6, and Greer tells him that the era of the nation-state is over. When Finch warns him that he's overestimating the power of AI, Greer says that's impossible He dismisses alliances as an allusion, and explains that he wants to live under a more just rule. Samaritan will make its decisions based on pure logic.
At the hotel, Sam tells Holcombe to draw his gun and cover her, and they move out. Collier's people spot them and open fire, and more Vigilance people close in from behind them. Collier shoots Holcombe, Sam is forced to take cover, and the Vigilance team grab Control and Rivera. One of their people activates the backup generator and Collier tells two of his people to take care of Sam, and then takes the elevator down with his prisoners. Reese arrives in time to take out the two Vigilance shooters, and they realize that Vigilance has something else planned for their captives. Hersh shows up and both sides draw on each other.
Root picks up her team and drives out of the city to New Jersey. The Machine reestablishes contact with her and Root realizes that she has to warn Sam and Reese.
Sam tells Hersh that they're there to save Control. Root calls Sam and tells her that Finch is in imminent danger. However, she now knows who the fifth Number belongs to: Greer. Vigilance is going after Greer, putting Finch at risk. Root warns that the Machine can't tell where Greer is, but tells Sam that Hersh knows. Reese asks Hersh if he knows where Decima is, and says that they can rescue Finch and Control if they work together. He lowers his gun and Hersh does so next, and then Sam.
Garrison meets with Greer at the office building, who describes Finch as the most important man in the world. Collier and his team break in and Collier is surprised to see Finch there. However, he's more than glad to have him and continue their last conversation.
Peter goes back to see Langdon but discovers that he's been reassigned to DC. The new AUSA, Janet Wirth, listens as Peter tells him that Jesse was meeting with a fellow AA member, not a terrorist. She offers her condolences but Peter says that Jesse killed himself because of them. Furious, he tells her that Jesse lost his family, his job, and his life. Janet claims that innocent people don't kill themselves, and a security guard comes in to remove Peter. Peter tells her that people without hope kill themselves, and the government stripped Jesse of his hope. Disgusted, he asks what that makes the government if they killed a man and walks out. As he leaves, Peter gets a text message from an unknown sender asking he wants to know what really happened to Jesse.
Reese, Sam, and Hersh make their way out of the hotel.
Root pulls over and the hackers tell her that the servers are ready. She points out a nearby car, gives them fake IDs, and says that they're part of the job is over. When they insist on seeing things through, Root tells them that the Machine has worked the math and if they go together then they all die. If she goes alone, she might survive. When they ask where she's going, Root points to a nearby building and says that Samaritan is there.
Rese and the others arrive at the office building. Collier has left a TV monitor and transmits a video message saying that he's been waiting a long time for this moment. He has rigged up a court room and has Finch, Greer, Control, and Rivera there. Collier announces that he is putting the U.S. government on trial for crimes against its people.