In one of the most depressing episodes, we find that the machine may have turned on them, causing the team to doubt their actions, and split up.
The episode opens with Shaw and Reese eating breakfast in a diner. They are talking about the surveillance machine. A car shows up and they meet up with two men outside, O’Neil and Ray.
Reese and Shaw put them against each other, and frame the scene to look as if they hurt each other. Root shows up, and takes Shaw with her to Alaska. She tells Reese that Finch needs his help in DC.
Reese and Finch speak about Samaritan and Decima’s plan to take over the machine. A new number shows up to Finch. It is Roger McCourt, US congressman from Illinois. He controls the flow of legislation. They believe Decima would want him dead due to his stance against public surveillance.
They find the congressman and take pictures to track his actions. Knowing that congressmen receive secret service watch when there is a threat against them, Reese pulls out a gun and fires towards McCourt, hoping the added security will help protect him.
Reese goes undercover as a secret service agent, stealing the identity of one named Abbot. Duran, McCourt’s driver, and a cop, wanted to be secret service at one point in time.
Bruce Dunphy, part of the leadership of Illinois machinist union, approaches McCourt at an opera theater, displeased with a deal he made. But McCourt tells Dunphy that he is working things out in his favor.
A man from Decima approaches the senator whose name came out in the leaked black budget report. The man tells the senator about Vigilance, and that they were involved in leaking the information about the surveillance system.
He gives him a picture of Collier, head of vigilance. The man scolds the senator for putting the country at risk with this machine.
He tells him that Decima has created another surveillance system. He asks him to approve their program, but the senator refuses.
Finch finds that McCourt has very few enemies. A homeless man meets with McCourt, who started a practice to give anyone a meal to anyone who needs one. It helps to maintain a good public image.
Reese finds a man spying on him, when he tries to approach him he gets away in a car and tells Finch the plate number.
Root and Shaw are at a bar in Miami, Florida. After taking down a group of men involved in transporting explosives, Root heads to St. Louis, and tells Shaw that the machine is sending her somewhere else.
Reese guards McCourt’s office, and hears a groan and load crash. When he enters, he sees McCourt about to have affairs with his aide. Finch finds that McCourt’s wife is aware of the affair, seeing that they have some sort of arrangement.
Finch also finds that the man, who was watching Reese earlier, drove away in a rental car set up by Decima. They believe that McCourt is a threat to the Samaritan system.
Reese spots them in the parking lot just as Duran receives a call, showing the real secret service agent who Reese is impersonating. Reese and Duran get into a brawl. Decima agents exit their car and start shooting at Reese. He manages to hit two of them, and gets in the car and drives away with McCourt.
Reese picks up Finch, who sees McCourt tied up in the back seat. With police and FBI after them, they dump the car and hide somewhere.
They talk to McCourt about Decima, explaining the situation, trying to find why they are an enemy, but McCourt doesn’t know anything about them.
Decima agents find them, and Finch sees that there is a tracker on McCourt’s suit. When trying to get away, another Decima agent shoots at Reese. The agent is hit by a car driven by Shaw, who picks up the guys just in time. Reese puts the agent in the trunk.
They run into a roadblock, set up to find McCourt. They stop before getting too close, and exit the car, bring the Decima agent with them.
They break into a house that is empty. They question the Decima agent. Finch discovers that the agent does not want to kill McCourt. Instead, he was sent to protect McCourt from Reese, Shaw, and Finch.
They find that McCourt has been making trades, earning big money from getting good inside information.
McCourt reveals that he knows Decima, and that they are working together. Decima uses McCourt’s legislative power to get Samaritan to pass, without him, they won’t get past congress.
Reese realizes that the machine gave them McCourt’s number because he was in need of protection, and the threat is Finch, Shaw, and Reese themselves. He thinks the machine wants them to kill McCourt.
They go back and forth about what they should do with McCourt. Finch tries to get McCourt to call of his deal with Decima, instead of killing him. After McCourt refuses, Finch offers him money instead, but McCourt will not back down.
Finch still tries to talk Reese out of killing McCourt, with Shaw taking Reese’s side. Finch tells them that the machine was for them to protect people, and if Reese kills McCourt, then he will have to leave the operation.
S.W.A.T. enters the house and they find the Decima agent and McCourt, dead.
Shaw, Reese and Finch are running away, but Shaw gets shot by S.W.A.T.
They get into a car with Finch trying to stop Shaw’s bleeding in the backseat. The next day, Reese, Finch, and Shaw are trying to hide from police who are looking for them. Reese is helping Shaw walk, Finch was following, but later, Reese and Shaw see that he is gone.
The senator speaks with the man from Decima again, and tells him that he will still not work with them. The man tells the senator that if they work with him, they will find him thousands of terrorists.
The senator gets a phone call, it’s from McCourt, and we see that this exchange had taken place before Reese shot him. It turns out that McCourt had already given Decima the go-ahead. The senator agrees and Samaritan is up and running. It’s first target, Harold Finch.