A mini-van explodes at a thruway rest stop killing the suburban mom behind the wheel. Booth and Brennan arrive on the scene, talking about how Caroline Julian has worked hard to get Brennan private visitation rights with her father, Max, at the Federal Detention Facility. Brennan doesn't want any special treatment.
There's explosive residue all over the van and metallic fragments in the bushes, suggesting a bomb was the cause of the explosion.
Brennan examines the badly charred remains and finds a locket with a picture of a little girl in a soccer uniform. Booth and Brennan wonder why anyone would want to blow up a soccer mom.
The blown-up mini-van has been brought back to the lab. Brennan and Zack remove charred remains, while Hodgins takes samples of residue to examine for explosives. Booth enters with Special Agent Katherine Frost, from the FBI bomb unit, who will oversee the investigation. Hodgins, who's clearly attracted to Agent Frost, learns they will be working together on the case.
Meanwhile, Booth has traced the van to its owner: Jeremy Nash in Culpeper, Virginia. Comparing Nash's picture to a charred photo found in the van, everyone concludes the woman driving was most likely Mrs. Nash. She was traveling with suitcases, filled with keepsakes and clothes. Was Mrs. Nash leaving Mr. Nash?
In a private visiting room, Brennan meets with her father, Max. Brennan wants answers, but all Max will say is that he's never hurt anybody who didn't deserve it. He asks Brennan if she brought him the deck of cards he asked for. Brennan hands him the cards and heads out. Max tries to stop her: the cards were for them to play their old game "Blitz". Brennan's in no mood to play cards.
At the Nash home, Booth speaks with Jeremy, who confirms the victim in the van was his wife, Amy. He tells us Amy was on her way to visit their daughter at college.
Back at the lab, Hodgins, Zack, and Agent Frost watch, Dermestes maculates, flesh-eating beetles, clean the flesh off Amy Nash's charred remains. Brennan enters with the news that Amy's left shoulder shows evidence of past trauma.
In the Keep, Hodgins tries to explain his attraction to Agent Frost to Angela. He tells her that his reaction is involuntarily. Angela understands: "as long as it stays in your pants." Hodgins asks her to take a look at some singed pieces of paper found in the van. There appears to be some kind of writing on them.
Zack is working in the bone room when Cam enters. She's found blue dye in the burned flesh from Amy Nash's sternum. Zack says there's also pitting on the manubrium. They'll have Hodgins try and determine what it is.
On their way to the forensic platform, Brennan and Booth discuss how difficult it would be to tell a child their mother is dead. Hodgins interrupts, he's found triphenylmethane dye and iron sulfate in the manubrium and the flesh. Both are ingredients found in ballpoint ink. It looks like Amy Nash had a homemade tattoo.
Booth, Brennan, Hodgins, and Cam are gathered around Angela and her computer. They attempt to make out Amy's barely recognizable tattoo. They see it's an inverted pentagram with a fist in the middle of it. It's the symbol of the National Liberation Army, a group of student radicals who, in the 1970's, used violence to try and change the world. The group was responsible for the murder of a cop in 1975. Two members of the NLA, June Harris and Neal Watkins were charged with the murder, but never caught. June Harris and the victim, Amy Nash have identical photos. Our soccer mom was a fugitive, a cop killer.
Caroline Julian storms into the lab, upset with the team's recent revelation. Turns out Caroline had negotiated the surrender of June Harris/Amy Nash. It was set to happen in four days. Harris was going to be cut a deal: nine years for killing a cop. The punishment was sure to upset Sam Reilly, the lead FBI agent on the case for the past thirty years. Booth leaves to find his old mentor, Reilly; his teacher at the academy. Meanwhile, Caroline wants Booth to get a hold of Leonard Huntzinger, June Harris' famously radical liberal lawyer.
At the FBI, Booth and Caroline talk with Sam Reilly. Reilly's just been told the news and is not taking it lightly. Begrudgingly, he passes the baton over to Booth, giving him a tip to ask Huntzinger about June Harris' old boyfriend.
In the interrogation room, Booth and Caroline ask Leo Huntzinger for information on Neal Watkins, June Harris' fugitive/ex-boyfriend. Huntzinger stonewalls. Reilly, who has been watching from the observation room, barges in and throws Huntzinger against the wall. In the commotion, Huntzinger throws a punch. When Booth threatens to arrest Huntzinger for hitting a federal agent, Huntzinger gives them a lead: the son of the cop Harris and Watkins killed, back in 1975, grew up to become a cop too. The other day he came after Huntzinger, wanting to know where he could find June Harris.
At prison, Max apologizes to Brennan for being such a horrible father: he wants to change things. He encourages Brennan to think about testifying on his behalf when he goes to court. Brennan can't help but feel like she's being used. "Is that why you finally apologized?" she asks as she storms off.
Back at the lab, Hodgins and Agent Frost are analyzing the bomb. They're getting along well, until Agent Frost attempts to throw out an air filter that was blown free from the van. Hodgins' is officially over her. How could she throw out evidence that may hold important clues to the case?
In the Bone Room, Zack shows Cam the soccer mom's reconstructed shoulder. Removing shrapnel from the bomb, he found fragments of lead in a copper alloy coating. Cam confirms that it's a bullet, but absence of fresh blood on her clothes and damage from the blast make it impossible to tell when the shooting occurred.
At the FBI, Booth, Brennan and Sam Reilly are on the way to the interrogation room. They're baffled by the bullet. Why would someone shoot Harris if they were just going to blow her up?
In the interrogation room, Booth, Brennan and Reilly talk with Danny Valenti, the son of the murdered cop. Records show Valenti had recently bought gas near June Harris' home in Culpeper, Virginia. Valenti claims he didn't know where she lived, only the town from the post-mark on the letter of apology Harris had written to him. Valenti was upset after reading the letter and admits he went to see Huntzinger, but that's it. Booth asks Valenti for his gun to see if the bullets match the fragments found in June Harris. Danny tells him to get a warrant.
Booth and Brennan arrive in Booth's office to find Reilly waiting, with a file in hand. The ballistics on Danny's gun did not match the bullet that shot June Harris. However, the bullet did match the gun used to kill Danny's father, thirty years ago. The same gun that was registered to June Harris' old boyfriend, Neal Watkins.
Booth and Brennan talk to Jeremy Nash. Jeremy tells them he only recently found out about his wife's secret past. Celia, their daughter, who has been listening in on the conversation, interrupts. She tells Booth and Brennan that the mother she knew was a loving and caring woman and not a radical cop killer.
In the Bone Room, Zack tells Cam the gunshot in June's shoulder was very old. Cam theorizes that since the bullet matches the same gun used to kill the policeman, June Harris may have been shot during the robbery in â€˜75. Zack makes another discovery. There are microscopic lead particles in on the metacarpals of the left hand. It's possible that the same bullet that shattered June Harris' shoulder first went through her hand.
At the Angelator, Brennan, Cam, and Zack, watch as Angela reconstructs the crime scene from the robbery thirty years ago. The scenario explains the gunshot wounds to June Harris. The squints believe June Harris, trying to protect the cop, raised her hands to stop Neal Watkins from shooting him, but that Neal fired anyway and the bullet ripped through June's raised hand before tearing into her shoulder.
Hodgins enters with news of his own. Not only did Neal Watkins shoot June Harris and the cop, but he also made the bomb that blew Harris up. Hodgins explains that a watch was used as a detonator in the explosion that caused June Harris' death. It's the same type of watch used by Neal Watkins when he made bombs for the NLA back in the â€˜70s. Everyone theorizes that Watkins killed Harris because he found out she was turning herself in. If Harris went to see Watkins before her death, Hodgins can use the mini-van's air filter, which is an "entomological GPS," to track him down.
Back at the lab, Booth tells Brennan to lighten up on Max, but she shrugs him off. It's clear she doesn't want to get hurt by her father again.
In Hodgins' area, Angela walks up and asks about the "bombshell from the bomb squad." Hodgins tells her that Agent Frost went back to the FBI and that it's a good thing, because she was starting to drive him crazy. Angela tells him the paper found in June's van was a letter, and that she's waiting for her computer to finish rendering it. Hodgins makes a discovery. The pollen in the air filter is Pinus appalachiana, Shenandoah pine, which is only found on Shenandoah Mountain in West Virginia. There was also crushed Pendleton leatherflower in the tire treads. These two clues tell him that Neal Watkins is most likely hiding out between the towns of Hendersonville and Maple Flats.
As Booth and Brennan drive to Neal Watkins, Booth tells Brennan that Reilly is meeting them there too. He explains the FBI tracked Watkins' location to a house registered to a Theodore Markham, an infant who died in 1953. Booth says Neal Watkins stole Markham's identity.
Booth and Brennan walk up to Neal Watkins house with their guns drawn. Booth senses something's wrong. It's too quiet. Inside, they stumble upon Sam Reilly standing over the dead body of Neal Watkins. Reilly says he knows how it looks, but that Watkins shot himself.
Cam examines the bullet wound to Neal Watkins and says it is consistent with a suicide. Brennan discovers Watkins had arthritis in his fingers, which proves he wouldn't have been able to pull the trigger. Zack points out that if he couldn't pull the trigger, he wouldn't have been able to build the bomb either.
At the FBI, Booth and Caroline talk to Reilly. It's not looking good for him. FBI found no evidence at Watkins' house that he made the bomb. There are also two American flag watches, confiscated from the NLA back in 1974, that are now missing from the evidence locker. Reilly maintains his innocence. Booth recommends he find himself a lawyer.
Back at the lab, Hodgins has discovered that the oxidation and bacterial erosion on the watch is inconsistent with a watch stored in evidence for thirty years. Because the watch was thirty years old, whoever made the bomb had to put in a new battery and left behind a thumbprint. FBI is running the print. Angela enters. She's completed the letter.
In the Bone Room, Brennan reads the restored letter written by June Harris to her daughter, Celia.
Booth and Brennan show up at the home of Jeremy Nash to arrest him for killing his wife. His fingerprint matched the one on the watch, Jeremy caves. He tells his daughter that June had still been seeing Neal Watkins over the years and using her family as a cover-up. He did it to protect himself and his daughter. Celia, who has been reading the letter, says that June was seeing Watkins because she was trying to get him to surrender too. That she was only trying to do the right thing. As Booth arrests Jeremy, Brennan takes the devastated Celia in her arms to comfort her.
Brennan is back at the prison where, once again, she attempts to reunite with her father. He asks her to play a game of Blitz. This time she says, yes.
Sam Reilly shows up at Booth's office with a bottle of thirty-year old Scotch. As the two raise their glasses in a toast to the end of the NLA case and the "changing of the guard" Reilly forgives Booth for arresting him. He would have done the same thing.
Outside the Lincoln Memorial, Brennan tells Booth that she has finally realized her father actually loves her. She's happy about the time she now gets to spend with him.