At the Medico-Legal lab BOOTH is rushing BRENNAN to leave so she can be an expert witness in a trial beginning in minutes. As she fumbles about gathering all her case files, she is bombarded by questions from all of her coworkers. She helps them as much as she can with Booth pressing her to leave. On the way out they run into DAVID SIMMONS, Brennan's latest love interest. He praises her latest manuscript, which surprises Booth, who was not allowed to read it. David reminds Brennan that she forgot something and when she runs back to her office she sees a digital reconstruction that ANGELA has just composed. Brennan orders her to turn it off and insists that her composition is incorrect. Brennan charges to the platform where ZACK was working with the skull that Angela used to make her portrait. She gets the artifact bag that is paired with this particular Jane Doe and takes it into her office.
In her office she digs into the artifact bag to find a few items, including a marble and a belt with a distinct dolphin buckle. Brennan knows this belt. She is devastated.
In the Angelator Room, Angela, Zack, HODGINS, DR. GOODMAN and Booth look at Angela's digital composite. They all want to know why it is such a big deal. Booth informs them that they have just found the body of Christine Brennan, Temperance's mother.
Brennan sits in her office looking at the other items in the evidence bag and Booth enters to console her. Zack enters and Brennan asks him for all the information he has on this body. He tells her that the body was found in a graveyard in Pennsylvania in 1998, but it was not in an actual grave. Someone secretly buried it there at the edge of the cemetery. Her body had been in storage at the Jeffersonian as long as Brennan had worked there. Dr. Goodman enters and recommends that Brennan go home and relax.
Brennan sits in her apartment reminiscing about her past, before her parents disappeared and she became estranged from her older brother. Booth arrives with some Chinese food from Wong Foo's and some information regarding Brennan's parents. He found the car that was abandoned the day Brennan's parents went missing and he's having it brought to D.C. He explains that he did some background checks and found that Brennan's father was a science teacher and her mother, a bookkeeper, was a witness for the prosecution twice which could have created some enemies. Booth also informs Brennan that her brother, Russ, is out on parole. Booth suggests that they get in contact with him.
At the Medico-Legal Lab Brennan is briefed by Hodgins who claims that her mother's body was buried for five years before it was discovered, but Brennan can't agree because her mother disappeared seven years before the body was found in 1998. Hodgins knows he's right, but suggests to Brennan that maybe he can find some fault in his tests. Booth arrives and the squints scramble. Booth tells Brennan that he has done a little more homework on who Brennan's parents were and has found that Christine Brennan didn't exist before 1978, meaning that name was a false identity. Brennan's parents weren't who she thought they were.
At a town carnival Booth finds Brennan's brother, RUSS, working as a ride repairman and shows him the composite of his mother. Booth asks him to help with the investigation in D.C., but Russ turns him down. After Booth threatens to turn Russ in for illegal repair operation, Russ agrees to help.
At the Medico-Legal Lab Hodgins shows Angela his latest findings on the soil surrounding Christine Brennan's body. He has found a movie ticket stub from The Fugitive, a movie that came out in 1993, almost two years after Brennan's parents disappeared.
On the observation platform Brennan is studying her mother's skull when Hodgins and Angela arrive to tell her about the movie ticket. Brennan is in denial, but Hodgins and Angela supportively assure her that this is the painful reality of her mother's death. Brennan swallows this and goes back to work on the skull. She looks inside to find a discoloration. Zack inspects it and agrees that there was internal bleeding in the skull.
Just then Booth arrives with Russ. Brennan can't believe her eyes. She doesn't want anything to do with Russ. She blames Russ for her parent's disappearance. She refuses to talk to him. Booth talks her down.
In Brennan's office Russ looks at the evidence bag that was paired with Christine's body. He remembers it all. It was his marble in the bag. Brennan tells him to put it back. Russ reaches out to the cold Brennan. She won't let herself befriend him.
In Angela's office Booth asks Angela to sit with Russ and draw up any descriptions that he provides from his childhood. Following that, he asks her why Brennan would let David Simmons read her new manuscript and not him. Angela's lips are sealed. Booth gets a call: the abandoned car has arrived in D.C.
In a spotless lab/garage, FBI agents search through different automobiles. Booth, Brennan, and Russ arrive to find their abandoned car. Brennan notes that their high school honor roll bumper sticker had the school name scratched out. The agents tell them that they found a bloodstain in the front passenger side. Booth goes through his new file and shows Brennan and Russ mug shots of their parents under the name Max and Ruth Keenan. They can't believe it. This means that Temperance Brennan isn't Brennan's real name. She was too young to remember, but Russ was seven. She knows that he must remember and this infuriates her. He tells her that his name was Kyle and her name was Joy. He has lied to Brennan her entire life. She slaps him and storms off.
At the Medico-Legal Lab Angela and Brennan talk on the catwalk. Brennan has come to grips with the fact that her parents abandoned her, and Angela consoles her. Brennan breaks down and admits that she admired her older brother and even made an identity out of being his little sister around town. She wasn't pretty or cool, so it was fun to be known as something. Booth shows up and tells Brennan that he's found the FBI agent that worked on tracking down her parents in the 70's.
In Booth's office at the FBI, Booth, Brennan, and Russ sit and listen to SPECIAL AGENT WARNER. She describes her work tracking bank robbers, including Brennan's parents, Max and Ruth Keenan. She explains that Max and Ruth were the smart crafty ones that ran in a brutish group of criminals. She never caught them. Booth and Brennan tell her that Max became a science teacher and Ruth, a bookkeeper. Warner figured that they pulled a job and then got killed for their cut of the profit. Then one of the FBI lab techs that was looking at the abandoned car enters to inform them that they've discovered blood from two different people in the interior of the car.
At the lab Hodgins has a digital reading of blood samples taken from Brennan, Russ, Christine and the other blood sample found in the abandoned car. Three match and one doesn't, which means that the fourth non-matching sample did not come from Brennan's father. They need to find out the identity of who this fourth mystery person.
In Angela's office, Angela asks Russ to describe anyone from his childhood that he felt may have been dangerous. Russ can think of one man. His father told him that if he ever saw that man come near the family again, to take Brennan and hide. Angela begins to sketch.
Late night at Brennan's apartment, she and Booth chow on some Chinese food from Wong Foo's. Booth knows that Brennan is feeling some disappointment in the fact that her family was a bunch of felons. She asks about Booth's parents who were regular folks, but he soothes Brennan by explaining that all parents have secret lives, that's what makes them parents.
At the Medico-Legal lab in the wee hours of the night, a restless Brennan arrives to find everyone still there working until they find out more about her mother's death. Zack explains that over his examination of the skull and suspect subdermal hematoma, there should be a larger injury marking. Brennan wonders if there was a smaller wound and maybe the subdermal hematoma grew over time. They magnify the skull picture and find tiny fractures that support that idea.
Hours later it is morning and Booth arrives to find Brennan asleep on her couch. Booth wakes her with the information that they've identified the other blood source found in the car. The down side is that it is someone in the witness protection program so he'll need to work at little harder to get access to his whereabouts. Then Angela enters to show them the composite she and Russ created. Booth bets that this is the man they're looking for and he exits to find out.
On the platform Zack has done more work on the damage he discovered on the skull. He's found a circular impact shape. Hodgins suggests a tire iron, but this mark seems too small. Booth has gotten the info he needs from witness protection and grabs Brennan to leave. She thanks the crew for everything they are doing before leaving.
Brennan and Booth arrive on a pig farm. They see their man, VINCE MCVICAR. Brennan finds three guns on him and tells him who she is. They ask him what happened to Brennan's parents. He tells them that he was running off with Christine and that Brennan's father caught them and attacked them both with a tire iron. He was knocked out and woke to find them both gone. He figured she was dead. Brennan has trouble hearing all this.
Brennan and Booth are back in her office and they've obviously told Russ what McVicar has said, but Russ doesn't buy it and neither does Booth. Brennan wonders why and Booth explains his theory of why the school name was scraped off of the bumper sticker of the car. He thinks that maybe while out one day, Brennan's parents find that they're being tracked by McVicar, who they know was the hitman of that crew, and they lure him away from Brennan and Russ and scratch off the bumper sticker so that they can never track down Brennan and Russ through their school. McVicar stikes, but only kills their father while the mother escapes with a head injury. Booth has the idea that they might find the murder weapon on his farm, something you use to bash in someone's skull. Booth leaves and Brennan and Russ argue about how they treated each other after their parents' disappearance. He reached out for her year after year, but she was never receptive.
Later, on the lab platform the crew goes over a dozen hammers and picks the one they confiscated from McVicar's farm. None of them match the mark found on Christine's skull. Booth reminds them all that using a hammer to bludgeon someone over the head would have been McVicar's signature method of murder as a hitman. Brennan wonders how one slaughters a pig because McVicar was a pig farmer.
Back at the pig farm with McVicar in cuffs, an FBI agent brings out a spring-loaded captive-bolt stunner. This device is pressed to the skull of a restrained pig and then punches a hole through, killing it instantly. Brennan knows that this is the weapon he unsuccessfully used on her mother. McVicar calls Brennan over. He tells her that there is no way she's ever going to be able to prove that he did anything. He says that if she quits the investigation now, he will tell her information about her parents that she would never find out from anyone else, but if she doesn't he will not go down quietly. Brennan trusts her skills as a forensic anthropologist and turns down his offer. She and Booth leave as McVicar is escorted away.
Brennan drives as Booth asks to read her manuscript. She refuses and tells him they are going visit Russ at the carnival.
At the carnival Brennan finds Russ and gives him his marble. She tries to reconcile with him and it is clear that this is all he's ever wanted.
Back at Brennan's apartment, Brennan, Booth, and Russ decide to crack some beers. As Brennan heads to the fridge Booth spots her manuscript and lifts the cover page to find that the manuscript is dedicated to Booth. This warms his heart until Brennan plays her answering machine. It is the voice of a distraught man, begging Brennan to end the investigation of her parents' disappearance. The voice is Brennan's father.