Reese and Sam are on the street watching the team's new number, clerical assistant Leona Wainwright. Finch tells them that Leona is in the Office of Personnel Management in DC and in NYC to see Mamma Mia on Broadway. They flip to see who will save Leona and Reese loses the toss, and goes over to the cab Leona has just entered. Sam notices that it has been sitting there for several minutes and sends the license number to Finch, who confirms that the driver isn't the man it belongs to. Meanwhile, the fake driver draws a gun on Leona but then sees Reese approaching. The man triggers a remote and the cab blows up, killing the driver and Leona. The killer's cell phone is blown kill and when Reese recovers from the blast, he grabs it.
Later at the library, Reese and Sam meet with Finch, who checks the cell phone owner and confirms that he's with Vigilance. As they realize that Leona is tied in with the Machine, Fusco calls from the bomb site and tells his teammates that the FBI has arrived and shut everything down. Root arrives at the street, posing as FBI agent Augusta King, and uses her fake ID to get past the security line. She tells Fusco that she'll handle it and warns him that Leona handled security clearances out of the OPM.
At the Pentagon, Senator Ross H. Garrison goes to see Control and demands to know if Vigilance is onto them. Control says that she'll send her people to Leona's office and collect any evidence the clerical assistant had. Garrison complains that Control lost Northern Lights, and she points out that despite that, they have stopped dozens of terrorist attacks. Control tells him to let her handle it and Garrison reluctantly agrees, but warns her that they can't let anyone learn of their connection to Northern Lights.
At the safe house, Finch gives Reese and Sam new identity papers and says that they'll be protecting their new Number, DA Matthew Reed. Matthew is going to Westchester for the weekend and they'll follow him there, and Finch assures them that the DA has no apparent connection to the Machine. Meanwhile, Finch will be going to DC to see why Vigilance targeted Leona... and will be taking Fusco with him. Fusco comes in to tell Finch that the car is ready and asks what music he wants on the trip.
When Reese and Sam track down Matthew in Westchester, they see him go into a high school and follow him. He's signing up for his 20-year reunion, and Reese and Sam discover that they're on the guest list as well thanks to Finch. The hostess, Alice, gives them itineraries for the weekend, tells them that local "hot dog king" Doug Hemmill will be handling the catering, and moves on. Sam is somewhat taken with Matthew, who comes over and greets her by her cover identity of Betty Harris. Once Matthew moves on, Sam checks the yearbook and discovers that in high school Betty had braces and glasses. She calls Finch, who insists that Betty had the closest facial structure to Sam of any woman who wasn't attending the reunion. Meanwhile, Reese is posing as Frank Mercer, a mattress king from Kenosha. The real Frank won a paid vacation compliments of Finch.
That night, everyone goes to local bowling alley, including local policeman, Jack Tanner, comes over and greets Sam. When he mentions that Matthew hasn't been back since graduation, Reese and Sam ask why and Jack says that Matthew's girlfriend Claire Klein died the night of the senior prom. Her body was in Matthew's car and everyone thought that Matthew was involved. Meanwhile, Doug is talking nearby to another returnee, Toke, who thinks that he knows Reese and comes over to invite him to get lit. Meanwhile, Matthew bumps into Doug who angrily tells him that he shouldn't have come.
In Washington, Fusco and Finch go to the OPM office only to discover that the FBI removing Leona's files. Finch, posing as Fusco's forensic photographer, manages to snap some photos of the boxes. He then goes into Leona's office with Fusco and they discover that the FBI have left nothing. Finch figures that Leona had the name of all government officials with access to confidential information and tells Fusco that the electronic copies of the files would be on the OPM's secure network. To access them, he'll need some time alone. Fusco assures him that he already has a no-tell hotel room lined up, but Finch suggests that he pay for a better hotel
At the bowling alley, Sam keeps eyes on Matthew while Reese talks to Toke. Toke tells Reese that Claire was dating Matthew but considered Doug her best friend. Matthew changed after Claire's death, but Toke figures that he had nothing to do with Claire's death by an overdose of hydrocodone. Another woman comes up to Reese and slaps him, much to his irritation. He calls Fusco and has him send the police file on Claire's death. Sam, checking around, tells Reese that the man he's impersonating, Frank, slept around with all of the women who have been slapping him as well as one of their mothers.
The lights in the bowling alley suddenly go out and the monitors light up with photos of Claire's dead body in Matthew's car. All of the attendees glare at Matthew, who walks out. Reese and Sam figure that the Machine was warning them that someone would want revenge for Claire's death and go after Matthew.
Sam goes after Matthew and, after secretly stealing his car keys, offers him a lift back to the reunion hotel. He refuses to discuss Claire's desk and goes to his hotel room. Sam claims that she's in the room next door, and then waits until Matthew goes into his room. She then orders the man in the next-door room out, claiming that the room has bedbugs. Once he leaves for the room Sam assigns him, Sam takes a shower and then hears a knock at the door. She answers it, gun ready, and finds Reese there. He points out that she sent the previous occupant to their room so he's staying with her. After they unpack their guns and toothbrushes, Sam runs an optic cable through the air vent into Matthew's room. According to the police report on Claire's death that Fusco has sent them, Claire died of a hydrocodone OD. Witnesses said that after prom, Matthew and Claire had a fight. Claire drove off and Matthew claimed he didn't see her alive again.
The next day in Washington, Fusco is enjoying the luxuries of Finch's five-star hotel and doesn't get up until 1 p.m. Finch has finished hacking the OPM computer system and discovered that the electronic copies were wiped as well. That leaves the papers that the FBI took. Finch has a portable package x-ray scanner and explains that he'll use it to crack the safe at the FBI evidence lockup... with Fusco's help.
That night, everyone gathers for the reunion dance at the high school gym. Doug is talking to another attendee, Phil, and Reese follows Doug. Jack comes over and tries to flirt with Sam, but Matthew rescues her and then invites her to dance. As they do, he wonders who she really is and Sam merely says that she's the one person who thinks that he's innocent. Sam figures that he really cared for Claire, but is hiding something else. As she asks for the truth, the balloons drop from the ceiling... along with a mannequin. The reunion attendees gather around it and discover that it has a nametag saying "Claire." Everyone turns to look at Matthew, who walks off.
Reese has been watching Doug and tells Sam that the man hasn't moved. He talks to Toke and asks if he's seen anything unusual, and the stoner admits that Phil is a lot heavier and taller than he was in high school. Realizing that Phil is an imposter, Reese moves on the man, who walks out and goes to the cafeteria kitchen. When Reese goes after him, the fake Phil attacks him. They fight and Reese gets the upper hand, but Toke wanders in and Phil grabs him as a hostage. Reese uses a plate to distract Phil long enough to knock him out with a food can. However, when Reese tries to interrogate Phil, the man commits suicide using a cyanide pill. Reese realizes that the fake Phil is with Vigilance, and warns Sam that the terrorist organization is after them, not Matthew.
Reese dumps Phil in the walk-in cooler and tells Sam that the Vigilance operative must have been running surveillance until they broke his cover. Sam looks around and realizes that she's lost Matthew in the crowd, just as several attendees complain that there's hydrocodone in their gift bags. Doug gets a text message on his cell phone and Sam picks it up via the cloning. It's from a "Claire" asking Doug to meet her in the chem. Lab. Reese and Sam realizes that Doug is the target and Sam follows him out of the gym while Reese goes directly to the chem lab.
When Doug gets there, he finds a suicide note on a table in his handwriting. Matthew comes in with a gun and explains that he plans to kill Doug as revenge for his killing Claire back in high school. The DA knows that after he and Claire fought, Claire went to her friend Doug for a sympathetic shoulder to cry on. Doug slipped her some hydrocodone hoping she'd pass out and he could have sex with her, but he gave her too much. Realizing that Matthew knows everything, Doug surrenders in the hopes that he'll go to jail. However, Matthew says that he's had to suffer 20 years under a guilty sentence, and now Doug will pay the price for his crime.
Reese and Sam arrive, guns drawn, and order Matthew to surrender. However, more Vengeance operatives break in and open fire. Everyone ducks for cover but Doug is hit in the leg. Sam gets over to Matthew and borrows her gun when she runs out of ammo. As she shoots, Sam admits that Matthew's scheme was well-considered, and admits that she has some problems with killing herself even though her friends keep telling her it's wrong. Matthew admits to her that he couldn't bring himself to shoot Doug. They're interrupted when Root calls to apologize to Sam. To trace Vigilance's encrypted signals, she leaked Sam and Reese's location to them so she'd have a baseline to decode it. As Root talks, she intercepts another encrypted Vigilance message, tells Sam that Finch is in trouble, and signs off.
At the evidence lockup, Fusco distracts the guard while Finch slips in and attaches the package scanner to the older-FBI safe without lead paneling.
Sam uses up the last of Matthew's bullets and improvises, creating a small bomb out of chemicals in the laboratory. She tosses it at the last shooter, stunning him, and Reese takes him out with his last bullet.
As Fusco tries to keep the guard distracted, they see Vigilance operatives breaking into the building. Meanwhile, Finch gets the door open and hears the explosion as the operatives blow open the door. He opens the safe and finds a file referring to Northern Lights... just as Collier arrives with Fusco as a hostage. Fusco explains that he surrendered rather than risk the guard's life. Collier figures that the government has a secret surveillance system that spies on everyone, and Finch used the information to get to Leona and the other people he and Reese have rescued. He orders Finch at gunpoint to hand over the file from the safe, and Finch has no choice but to do so. As he does, Finch warns Collier that if he jeopardizes the system then he's putting everyone at risk. Collier points out that thanks to government abuse of power, everyone is already at risk and tells Finch that he's coming with him for further interrogation.
As Collier escort Finch out, Root arrives and takes down the men holding Fusco. Collier runs off and Root identifies herself with her fake FBI ID when the security guards arrive. She checks in with Sam, who is with Reese watching Jack haul Doug off to jail. Matthew approaches Sam and tells her that he's going to make a full confession and that he might end up serving some jail time. He suggests that they hook up once he gets out. When Sam tells him that she doesn't do relationships, Matthew tells her that's not what he was looking for.
Finch, Fusco, and Root leave the building and Root admits that the Machine has been unable to locate Collier. As they talk, Root intercepts another encrypted Vigilance transmission: "Disseminate."
Later, news channels are reporting on secret government files confirming the existence of a massive surveillance program. Garrison holds a press conference claiming that the program doesn't exist. Afterward, Garrison goes to Control and tells her to terminate Northern Lights. When she balks, Garrison threatens her, leaving no choice. Once he leaves, Control gives the order to shut down Northern Lights... and then shreds her file on Collier.
Finch and Root are walking and Finch explains that he'll be staying in Washington as long as Vigilance is active there. Root suddenly stares off into space as the Machine reroutes the relevant Numbers to her now that Northern Lights is shut down. She smiles, tells Finch that she's going to be very busy, and walks away.