911 gets a call from a boy that his brother has been shot.
Reese and Finch return to the library and Finch nervously checks to make sure that the mystery hacker, Root, hasn't left any surprises for them. While he rebuilds the electronic and computer defenses, Finch tells Reese to check on their next number: 14-year-old Darren McGrady. Reese goes to Darren's last address and discovers that there is police tape across the door. Finch assures him that Darren's situation is ongoing and Reese finds blood on the floor as well as photos of Darren with an older boy. The superintendent comes in and Reese poses as a police detective. The man tells Reese that Travis McGrady, Darren's older brother, was shot a week ago and the cops took Darren away.
The next day, Reese meets with Carter. She pulls up the file on Travis and confirms that three gang-types shot him and ran. It took a half-hour for first-responders to show up after Darren called 911, and the parents died several years ago. Darren went missing after waiting all night at the precinct for Child Services. As Reese starts to leave, Carter asks him how he comes up with the numbers. Reese doesn't answer and Carter agrees to talk to the detective in charge of Travis' case.
Carter talks to Detective Hill, who wonders why she's bothering with such a minor case. He explains that Travis was working the late shift at a fast-food joint and got into a fight with three males over a waitress. Travis tossed one of them out and the three guys were the ones who shot him later. No one is testifying and Hill doesn't see the point in trying to track down Darren.
Reese goes back to the library and worries that the gang members will go after Darren next if they think he saw anything. He goes to talk to the waitress, Lisa, who is clearly afraid. Reese reminds her that Travis helped her and asks her to point him in the right direction. She suggests that he go to a local comic book store where they hang out. Reese goes to the shop and notices that the owner, Mr. Wilcox, is handing out free comics to the neighbor kids. One of the shooters, Brick, comes out, bumping past Andre, and Reese calls Carter to tell her where Brick is heading. However, Darren approach Brick and draws a gun on him, and demands his brother's stolen hat back. Reese intervenes and disarms Darren before he can shoot, and tells Brick that if he has to shoot then he won't miss. As Carter pulls up, Brick promises Darren that he and his gang will be looking for him. Carter arrests Brick while Reese takes Brick's cell phone and leaves with Darren.
Once they're clear, Reese explains that he's not a cop and figures that Darren pawned everything he owns, including the trumpet he owns, to buy the gun. Darren explains that his brother wanted him to go to medical school, and Reese points out that now he's involved with the gangs. He says that he'll take care of the gang and takes Darren to a youth group home where Fusco is waiting. Fusco warns that Carter is going to catch on if he keeps running Reese's errand, but Reese says that he'll take care of Carter. The detective has made arrangements with the woman who runs the home to take care of Darren without filing the paperwork. Reese then goes through Darren's sketchbook and finds a drawing of Brick.
At the precinct house, Carter tells Brick that they're going to run the DNA on Travis' hat, but Brick knows it'll take months to run the tests and asks for his phone call. In response, Carter tells him that he'll get out when she takes him to her arraignment.
Reese goes to the basketball court in the sketch and takes photos of the gang members there. He spots one of them, Curtis, calling a number and picks it up on Brick's cell phone. They then get into a nice car and Reese figures that they've got some kind of operation running. He calls Finch to run a check, but the hacker says that he'll need a couple of hours to get his hardware replaced. Reese wonders if everything is all right and Finch says that it is.
Once Finch hangs up, he looks up from the desk in his expensive office as the receptionist brings Will Ingram in. Finch assures him that his insurance business is doing fine, and Will says that he's found a few interesting things in his dead father's belongings. He show Finch a champagne cork wrapped in a piece of paper with the words "Day One: The Machine--January 24, 2005" on it. Will explains that the date is right in the middle of the period when his father shut down the company. Finch feigns ignorance and Will says that he's going to talk to Alicia Corwin, the only name in the files during the blackout. She quit her government job a year ago and moved to Green Bank, WV: the only town in the U.S. with no cell phones or wireless Internet. Also, Will knows that his father signed the $1 contract with the government one day after the note was written. Finch suggests that they get lunch and secretly pairs Will's cell phone. As they leave, Fusco takes photo of them. However, he gets a call that Darren has left the home.
Reese is watching Curtis when Fusco calls to tell him that Darren is missing. The detective says that he's too busy following Finch, and Reese notices a bar in one of Darren's sketches.
At the bar, Darren goes in and demands to know where Curtis and his partner Trim are. Two thugs take offense and start to attack Darren, but Reese arrives and takes them both out. He then hustles Darren out and goes to a diner. As they order, Reese tells Darren to promise to stop looking for his brother's killers. In response, Darren gives Reese all the money he has left to take down the killers. He says that Reese must be a ronin: a masterless samurai who wanders the land helping people. Reese says that he's not hired, but Darren says that he has a better chance of staying alive if Reese is with him. When Reese realizes that he won't convince Darren to stay low, he gives Darren all of his money back except for a quarter and says that there'll be no killing.
Reese and Darren follow Curtis and Trim, and Darren insists that Reese should be acting instead of watching. In response, Reese says that observation is the key. He watches as the gangers collect protection money from businessmen, including the money they get from running lottery tickets through the stores. Darren warns that the cops don't care and are probably paid off, but Reese figures that they can handle them now that they know where they're getting their money.
Reese goes to the gangers' SUV, breaks in, and drives away. He then calls Darren and tells him where to meet him. They meet and Reese explains that he stored the car and wanted to shake things up. He then calls Finch and has him put a GPS on Curtis' cell phone. Finch is worried about Darren, and Reese complains that Finch keeps disappearing on mysterious business. In response, Finch ignores his complain and sets up the GPS.
As they continue, Reese admits that he's killed people, and not all of them were bad. Darren figures that someone tricked Reese into killing good people. They find Curtis and Trim again and Reese explains that they need to find their weak spots. Trim tells Curtis to get his grandmother's car and meet him at their boss, Andre. Reese tells Darren that now they have to find the boss and hurt him.
Captain Womack asks Carter how long she's going to hold Brick, and warns her that she has until 5 the next day to arraign Brick or kick him.
That night, Curtis and Trim go to the comic book store as Reese and Darren follow them. Reese realizes that Mr. Wilcox, Andre, is their boss. Andre takes them inside and says that he'll take care of Brick. They claim that they switched cars but he figures that they're lying, and tells them to do whatever he tells them. Andre orders them to deliver the money to Brighton Beach or he'll kill them, and Reese and Darren follow them.
As Curtis and Trim drive down the street, Reese rams them with Trim's car, gets out, and tells them that he's found their car. The next morning, two cops get into their car and find Trim in the back, naked and covered in beer bottles. When Carter calls Reese to complain, he assures her that Darren wasn't in the car when he rammed the gangers. She tells Reese that Womack thinks that she released Brick when she hasn't, and Reese tells her that he's going to go to work on Curtis. He asks Curtis for the gun they used to kill Travis. When Curtis denies everything, Reese lights up a blowtorch, and then says that the money is supposed to be in Brighton Beach. He figures that Andre will believe Curtis stole the money, and the only way he'll survive is if he comes back with the money. When Curtis still doesn't talk, Reese starts burning the money. The ganger finally cracks and tells Reese that the murder weapon is in a chimney on top of his grandmother's building.
Will meets with Alicia in the park, unaware that Finch is following him. He asks her about the cork bottle note and asks about the $1 contract. Alicia asks Will if he's really sure if he wants to know and he does, and then she tells him that IFT was going to go bankrupt, and she persuaded the government to bail him out for $1. Will isn't convinced and wonders what it has to do with the Machine mentioned in the note. Alicia says that Nathan was in a dark place and advises Will to let it go. When he mentions Finch by his alias, Alicia is surprised to hear about him, looks around nervously, and quickly walks away.
Andre meets with Captain Lynch and demands help, but Lynch reminds him that their arrangement doesn't include force majeure. He tells Andre to fix it and fast, and Andre says that he'll handle it on his own. However, he wants Lynch to get Brick out of jail and the captain says that he'll see what he can do. Lynch goes to the station and says hello to Fusco as he goes by. Carter notices and wonders that Fusco and Lynch are friends. Meanwhile, Lynch talks to Womack, who tells Carter to release Brick immediately.
Reese and Darren go to the chimney and recover the gun. Darren wonders what will happen to Andre, but Reese points out that Andre didn't kill his brother. When Darren figures that he's just as bad, Reese says that it won't stop there and none of it will bring Travis back. He asks Darren if that's what Travis wanted for him. Reese then calls Carter with an anonymous tip, but she admits that she released Brick ten minutes ago. He realizes that Brick will be able to ID Darren to Andre, and then discovers that Darren has slipped away and taken the murder weapon with him.
Reese calls Finch and tells him to get the bag that he has prepared for Plan B. Meanwhile, Fusco spots Carter leaving and offers to go with her and help. She agrees and the two of them slip out when Womack isn't looking.
Darren slips into the comic book store and confronts Andre and Brick. The boy draws on them.
Outside, Finch meets Reese with the bag, which contains a rifle loaded with bean-bag ammo. Reese gives Finch a pair of bolt cutters and tells him to cut the power.
Andre tells Darren that he's brave and invites him to shoot Brick. The comic book owner tells Darren that he'll be doing him a favor and tells the boy that he's got the conviction to do it, and then come work for him because he's smarter than the rest. Darren aims the gun but then refuses to shoot. Andre takes the gun from him and says that comic books teach kids about revenge, but it's not reality. The power goes out and Reese storm in, shooting down the gangers.
As Carter and Fusco pull up, they hear the gunshots and call backup. Andre comes out, using Darren as a shield. Carter manages to wing him, making him lose his grip on Darren. Fusco tackles Darren, taking a shot in his rear, while Reese shoots Andre and knocks him out. The police arrive and take the gang away, while Darren thanks Fusco for saving his life.
The next day, Finch meets with Will, who explains that he's taken a job in Sudan. Finch asks if Alicia told him what he wanted to know, and Will admits that it's hard to believe that Nathan was an ordinary guy. In response, Finch tells him that Nathan always said that Will was his proudest achievement. They hug and Will takes off.
Reese drops off Darren and tells him that Fusco has a lead on good foster family. When Darren wonders what happens if they're not, Reese tells him that he'll take care of it for him. Darren gives him a sketch he's made of himself and Reese in heroic poses. Reese thanks him and says that he'll be starting at a music charter school, and gives him his trumpet back. Darren tells Reese that someday he'll find a home too and goes into the group home. Once they're alone, Fusco warns Reese about Carter again and then reports that Finch's oldest identity as Harold Wren is an underwriter for an insurance company. He met Nathan at MIT and they graduated in the same but Fusco has confirmed that Wren is an alias as well. Reese concedes that Fusco would have made a good cop if not for a few bad choices, and Fusco points out that Reese is the one who has Fusco snooping on Finch.