A woman gets out of her van, looks over at a bunch of children and then enters again. She pushes a paper a little further into her purse. While leaving the parking space and going onto the road, the car explodes.
Booth and Brennan arrive on the scene. While checking the scene out, Booth and Brennan argue about her father and about how after she got her private visitation permission, she refused to visit. Brennan refuses to let the explosives lab take the van and demands that it be transferred to the Jeffersonian to analyze the body parts that were scattered all around it. They find a locket containing a picture of a young girl and assume that it's the victim's daughter.
At the Jeffersonian, the team tries to gather information from the van. Angela tries to make a facial reconstruction and Hodgins takes the steering wheel to check for fingerprints. Booth enters with an explosive expert, Special Agent Katherine Frost, and they team her up with Hodgins who is obviously attracted to her. Booth checks the plate number; it is registered to Jeremy Nash in Virginia. Cam says that Jeremy Nash is the husband. Booth wants to take Brennan to and go talk to him but she says that she's going to see her father so he goes alone.
At prison, Brennan talks with her father about how he was a criminal and a not-so-good father. He tries to make things work with her but she's stubborn and doesn't give him a chance. He asks her to stay a little and play cards with him, but she tosses him the deck and leaves. On her way out, he asks her to bring him some socks because his feet hurt.
Booth interrogates Jeremy, who is very upset. He tells Booth that all the personal stuff his wife was carrying in her car was there to be put in their daughter Celia's dorm room and not because the couple had marital problems. Zack and Hodgins show Agent Frost bugs which she considers fascinating when Brennan walks in and Hodgins begins to ask about her father, but she cuts him short. Hodgins leaves after Brennan notes that he's not currently doing anything useful with Agent Frost. He goes to see Angela, who's working on the Widow's son case, and she tells Hodgins that she's okay with him being attracted to Agent Frost as long as nothing happens between them. He gives her pieces of burnt papers that Cam wants her to put together. Hodgins tells Booth and Bones that the victim, Amy Nash, had a tattoo. They all go to Angela, who helps them discover that the tattoo was of a revolutionary gang back in the seventies. They then look up the victim and find out that she's actually a convicted killer on the run for killing a cop during a robbery 30 years earlier.
Caroline goes to the lab and says that Amy Nash or June Harris (her name back in the revolution) was about to turn herself in. Sam Reilly (the agent in charge of the case for 30 years) is mad because he didn't know anything about that until now. Booth interrogates Attorney Huntzinger, the victim's lawyer. During the interrogation, Sam Reilly bursts into the room and attacks Huntzinger, who hits back and is arrested for hitting a federal agent. He tells them that they should be talking to the murdered cop's son, Danny Valenti, instead, and he shows them some bruises that Danny gave him for not revealing June's location.
Brennan goes to her father in prison again to give him the socks he requested. He apologizes about being a bad father, then he asks her to testify for him in court. She accuses him of apologizing just to get her to testify for him. Brennan gets really angry and leaves.
Back at the lab, Hodgins gets really angry with Agent Frost after she nearly throws away the van's air-filter. Zack tells Cam that June was also shot, but he doesn't know how long ago yet. Sam argues with Brennan about Danny on the way to interrogating him. Booth takes Danny's gun to check if the bullet June was hit with came from it.
The gun is checked and it is not the one used. But, the bullet June was shot with was the same one that killed the cop. Booth and Brennan go talk to Jeremy about Neil Walkins, June's ex-boyfriend and partner in crime. He says he's heard of him before, and also says that he talked his wife out of talking to a federal prosecutor.
Zack finds out that the bullet hole is very old, and that there is another identical one in June's hand. Angela recreates what happened the night of bank robbery. They conclude that Neil is actually the one who killed the cop and that June tried to get in the way to protect the cop, but was shot. Hodgins figures out that Neil is the one that made the bomb; the watch had his trademark which was the American flag. Hodgins finds out where Neil lives, while talking to Angela about Agent Frost and telling her that he's no longer attracted to Frost.
Booth and Bones go to see Neil's and plan to meet Sam there. They walk in and find Neil dead with Sam pointing a gun at him. Sam says that Neil killed himself but Booth arrests him anyway. Brennan finds out that Neil had a disease that would prevent him from pulling the trigger. Booth tells Sam to get a lawyer. After Hodgins inspects the watch a little more, he finds the battery had Jeremy's fingerprints. Booth and Bones go to arrest Jeremy, who admits being guilty, and says that he caught June going to see Neil. Brennan gives Celia the letter her mother left for her, which explains that June was actually trying to get Neil to turn himself in too.
After reading the letter, Brennan goes to see her father in prison and they play cards. Sam invites Booth to a drink that he was saving until the case was closed. A drunk Booth is sitting with Brennan, and he talks about how he loves America and Brennan says that she now believes that her father does love her.