Reese meets Finch at a diner and asks what's good, and Finch accuses him of trying to find out more information about him to learn who he really is. He gives Reese a menu and walks away, and Reese finds a photo of Judge Samuel Gates in it. Reese goes to watch Gates, who lives with his son Sam Jr. His wife Elizabeth died of brain cancer a year ago and Sam is all that Gates has left. The nanny is Christina Rojas, who Gates hired when Elizabeth was diagnosed with cancer.
Reese watches Gates in court and figures that the judge is a victim rather than a perpetuator He's reputed to have a lot of enemies because of his tough stance on crime. Reese then breaks into Gates' office, checking his computer and planting bugs. He finds a file filled with death threats and gets them to Finch, who identifies six possible suspects. Meanwhile, Reese watches Gates and spots two men following him. He goes in pursuit but one of the men gets a call, tosses the phone in the garbage, and both men walk away from Gates. Reese collects it and confirms it has a message saying that the son is out from school, and Reese figures that they're watching the wrong Sam Gates. He gets to the apartment just as three men try to abduct the son. One of them, Drost, manages to shoot Reese, grazing him in the shoulder, and they drive away.
Back at the library, Finch insists that Gates is in danger and the Machine is correct, and figures that the kidnapping plot ends in Gates' death. Reese says that his plan is to find Sam and return him to his father.
Gates receives a call from the kidnappers. They tell the judge not to tell anyone and to wait for their next call. When Gates tries to negotiate, the head kidnapper hangs up. As Gates calls to determine if Sam is safe or not, Reese approaches the judge and says that he's here to help him. Gates figures that Reese is with the kidnappers, but Reese assures him that the kidnappers want something and will try to negotiate. The judge demands answers but Reese tells him to focus on getting his son back.
Reese and Gates go to the judge's home and discover that Christina is gone. Gates insists that Christina loves Sam and wouldn't be involved in the kidnapping. Reese confirms that Gates hasn't tried any cases involving kidnappers, and the judge explains that he hasn't. Once he leaves, Reese sets up surveillance and ignores Finch's warning that they don't want to have a judge scrutinize them. He then goes to Christina's apartment, finds her body, and removes a bullet from the wall. Reese figures that the kidnappers tortured Christina for the alarm codes. As he works, Reese talks to Finch, who says that he's tracing the cell phone that was used to make the call to Gates. However, Finch warns that it will take some time to hack the phone company's firewall. Reese calls 911 and leaves without saying anything.
At the station, Fusco goes through Carter's desk and spots the photos she has of Reese. She comes in and he manages to put everything back where it belongs. Carter asks why he's there and says that she's heard rumors of his illegal activities at the 51st. Fusco gets a call and offers to get her a cup of coffee. He goes to meet with Reese at a coffee cart, and Reese gives him the bullet to have him check it with Ballistics. He wants to know about Carter and Fusco warns that she won't give up. When Fusco wants to know more about the kidnapping of a child, Reese slips away.
Finch finally hacks the phone records and tracks the purchase to one of the men. Reese attacks the man outside of his apartment and knocks him out. He confirms the man, Leon Josef Turski, is part of a SP-9, a Eastern European street gang that ran kidnappings. Reese figures that they've opened a branch in the U.S.
Detective Olson investigates Christina's death and calls Carter in when witnesses confirm that a man matching Reese's description was there. They both wonder why Reese was there, and send a cop to see Gates. Gates claims that Sam is upstairs in his room and the cop leaves, and Gates tells the listening Reese that Christina was there the night that Elizabeth died. Reese assures the judge that Sam is still alive and asks for his help. He asks what Gates knows about SP-9, but the judge questions whether Reese can get back his son. Reese says that he can remain invisible and that he's the best chance that Sam has. As Gates says he hasn't heard of SP-9, the kidnappers call. They put Sam on the line briefly to confirm that the boy is alive, and then the head kidnapper says that they want Gates to dismiss a case against Angela Markham. If she doesn't walk, Sam dies. Once the kidnapper hangs up, Gates tells Reese that Angela ran over a man in a parking garage.
The next day, Gates tells Reese that Angela is an account executive and hit a CPA after drinking heavily at a company party. Reese warns that the kidnappers will eventually kill gates as well to cover their tracks, and he needs a way to hurt them. He tells Gates to stall and buy Reese time to check SP-9 out. He meets with Finch, who has confirmed that SP-9 is active in 18 countries and have almost no digital footprint. Reese has him focus on Angela and suggests that she's sleeping with someone in SP-9. Reese then checks on Turski, who is locked in his trunk but still refuses to talk.
Fusco talks to Carter, who is examining the bullet holes from Christina's apartment. Reese calls and Fusco admits that they don't have anything, and offers to do what he can to ID the nanny's killer. Once Reese agrees, Fusco goes over the murder scene photos with Carter and points out that the evidence shows that the killer is a pro. Impressed, she invites him to help.
While Gates convenes his court, Finch comes in and pairs Angela's phone. He then goes back and begins driving his car around at high speeds to torture Turski. Turski insists that he knows nothing about Sam or Angela, and explains that SP-9 works in cells and only uses street names. He finally gives Reese an address where he goes to get paid, and Reese leaves him in the trunk.
Gates tries to stall the case as much as possible, sustaining the defense's objections. When the prosecutor objects, Gates tells her to take some time to prepare her witness and ends the case for the day. He goes to his office and receives another call from the kidnappers. The head kidnapper says that he's disappointed that Gates is stalling and tells him to finish the case and fast. Once Gates hangs up, he receives a photo of Sam on his cell phone. Meanwhile, Finch confirms that Gates receives the call and follows Angela. He calls Reese, who brings him up to speed. Finch then intercepts a call from the kidnapper to Angela. The head kidnapper insists that their operation is in jeopardy because she got drunk, but Angela says that she'll go back to work once he gets the charges dropped.
Reese goes to the apartment and Drost spots him. Reese subdues him and knocks him out when he refuses to talk. He then breaks into the apartment and discovers that SP-9 is running a money-laundering operation.
Soon the head kidnapper is making calls to determine who stole his half million in laundered money and made two of his men disappear. Reese takes the money to the library, and Finch explains that she's tracked Angela's activities and confirms that she works at a tech company that makes banking software that can spot money laundering. She oversaw the installation of the software at Onestate Bank, and could turn the whole system off and let SP-9 launder safely launder the money. If Finch can access the accounts and learn what SP-9 finances, they can track down where the gang is holding Sam.
Reese meets with Gates at the courthouse and tells him that they're close. Gates refuses to cooperate but Reese asks him to trust him. Back in court, Gates reverses his decision on the video's admissibility and refuses to grant a mistrial. The prosecutor, Monica Ramirez, demands an explanation but Gates tells her to drop the matter or she'll find out how far he's willing to go. Ramirez concludes her case.
Finch goes to Onestate posing as a programmer and accesses the computers. When another programmer asks why he's there, Finch bluffs it out and says that the system has been compromised, and that he'll be taking the man's job.
Reese tosses Drost in the trunk with Turski and demands answers, but they both refuse to talk. Reese then unties Turski, tells him to get the boss' name, and locks them both up in the trunk.
At the station house, Fusco finds security footage of Christina's house on the day of the murder and spots the killer. When Carter wonders how he's so sure that the man on the camera footage is the killer, Fusco explains that he ran the man's license plates and connected them to a company, Coldfield Holdings in Brooklyn. Carter figures that they should give it a look, and Fusco secretly calls Reese.
Turski gets the name of the boss, Jarek Koska, and gives it to Reese in return for a hamburger. Reese passes it on to Finch, who is unable to connect the kidnapper to the accounts. Finch confirms that Angela shuts down the system for three minutes every day, giving SP-9 the opportunity to launder millions for themselves and hundreds of their criminal clients. He warns that it could take hours to track down the shell company, just as Reese receives a text message from Fusco about Coldfield. He gives Finch the name, and the programmer confirms that it's a large account used to buy real estate in New York. He sends Reese the address of an abandoned church purchased two days before Angela went on trial and within 10 blocks of Gates' home. As Finch sends Reese the address, he warns that the jurors are ready to render a verdict.
Reese goes to the address and tells Finch to call 911 in four minutes if he hears nothing further. When he goes inside, he finds nothing but a discarded blanket. Finch is at the courthouse and watches as the jury declares Angela not guilty on all charges.
After the trial ends, Gates goes outside and receives a call from Koska. Koska tells him to come alone, while Finch watches. He gives Reese an update, and Reese warns that Gates won't listen. He then abducts Angela from outside the courthouse.
Koska and his men meet with Gates at a park. Koska gets Sam out of the SUV and prepares to shoot him, and Gates offers himself. The kidnapper isn't interested, but Reese arrives with Angela as a hostage, and says that he knows who Koska is and has all the details of his operations. When Koska prepares to have him shot, Reese says that he's not alone. Koska receives texts confirming that all of his money has been transferred to an offshore account. If he doesn't cooperate, Reese says that he'll notify all of Koska's clients that he lost their money. Koska tells his men to kill everyone, but Reese takes him and his men down. He tells Gates to take his son home and then informs Koska that they'll be going for a little ride.
At the courthouse, Ramirez receives a complete file on Angela's crooked dealing at Onestate. Finch quietly slips away.
Fusco and Carter go to the killer's address and find Koska, Angela, and the other kidnappers tied up and seated next to the laundered money. As the police take them away, Reese watches from down the street.
Later, Gates and his son are playing soccer in the park. Reese approaches the judge when he's alone, and Gates thanks him for his help. He warns that people will eventually find out what Reese does and that there's nothing he can do to protect him. Reese simply tells him to play with his son and walks away. He goes to the diner and meets with Finch, and tells him that Gates said that he might help him some day. When Finch says that he listened to the conversation, Reese says that he read between the lines. He then thanks Finch for giving him a job. Finch, taken aback, tells Reese to try the eggs benedict and says that he's had them there many times.