There's a battle brewing on the paintball field. Camouflaged soldiers run around, splatters of paint hitting them left and right. One solider, Buster, breaks off from the group to find safety. His plan backfires and he is pelted with colored paint. He falls, his mask obscured by paint, next to another person. Buster believes it's another solider until he touches the person's rotting face and realizes his fallen comrade is really a corpse.
Booth and Brennan make breakfast in Booth's crowded kitchen. The couple has decided to split their time between each other's places, but the arrangement isn't working. They discuss the possibility of having one place they can call home. They are interrupted by Booth's phone...there's a murder to be solved.
Booth and Brennan join Hodgins at the crime scene. The body is in a shallow grave, covered with coffin flies. Hodgins determines that time of death was around seven days ago. Brennan identifies the victim as a female in her late twenties to early thirties. She also notices that something was jabbed through the victim's hard palate into her brain. Due to a surge of pregnancy hormones, Brennan cries as she makes her observations. Booth tries to capture the rare moment with a few photos on his phone. Brennan leaves the crime scene in tears, and requests the remains be sent to the Lab.
At the Lab, Cam cuts through the skull to get to the victim's brain. Wendell nervously watches over her, as Brennan has instructed him to make sure the remains aren't compromised. Hodgins notes that the victim has an oily residue on her clothing. After Cam removes the brain, she finds tiny beetles in it. Hodgins is delighted and puts them in a jar. They may have ingested particulates from the weapon! Wendell notes markings on the top of the skull, which he believes were caused by the murder weapon. Because the brain tissue is torn, Cam adds that the weapon was most likely made of metal and had a jagged edge.
Booth tells Sweets they are checking the paintballers' alibis. Sweets tries to pry into Booth and Brennan's living situation, but Booth won't divulge any details. Although Sweets is eager to help, Booth tells him to stick to the "shrinky stuff."
Angela takes pictures of the remains for her facial reconstruction. Brennan and Wendell determine there is damage to the left side of the victim's frontal bone, clavicle, and acromion. There are also remodeled fractures on the skull, which could be from a fall or beating.
Hodgins tells Cam that the victim's clothes were soaked in linseed oil, a substance that would have kept the victim dry. Also, the beetles from the brain contained traces of Lorazepam, which is prescribed for anxiety. Cam has discovered past brain damage that compromised the victim's cognitive functioning. Perhaps this is why she was taking Lorazepam?
In Angela's Office, Brennan confides that she is not ready to move in with Booth. She has always been on her own. Angela tells Brennan that she will never be alone again. She takes Booth's side. Angela plays a home movie of herself with her new family. Brennan is touched by the video of the Hodgins family and feels affection for her friend. Angela shows Brennan the finished facial reconstruction. Their victim is Claire Serrano. She's been reported missing twice in the last six months.
Sweets and Booth talk with Pastor Joseph Serrano, Claire's husband. Joseph explains that Claire disappeared last February, but returned six weeks ago. She didn't remember who she was or anything about her life. This sounds familiar to Sweets: retrograde amnesia. Claire suffered head trauma and established a new identity as a survival technique.
Booth and Brennan have lunch at the Diner. Booth wonders if Joseph Serrano could have caused Claire's injuries. Brennan chows down as she reveals that she is ready to move in with Booth. Booth is ecstatic until Brennan stipulates that Booth must move into her apartment. After all, Brennan is more rational, financially secure, and she is carrying the baby. Booth does not agree. This should be a family decision. Sweets arrives with information about Dr. David Yazrick, a psychologist specializing in memory problems. He was treating Claire. Sweets senses the tension so Booth suggests they head out to meet Dr. Yazrick.
In the Lab, Hodgins tells Wendell that the soil at the bottom of the grave contained cotton fibers coated in linseed oil. They aren't from the victim's clothing. Hodgins doesn't know where the fibers could have come from, but whatever the item was, it was removed before Claire was buried. Someone may have dug something up.
In Booth's Car, Sweets describes Dr. Yazrick's methods. They're a little unorthodox. Booth recalls that Dr. Yazrick was thrown out of a casino for counting cards. Yazrick claims it was for research but some believe it was a publicity stunt. Sweets wants to discuss the incident at the Diner, but Booth is tight-lipped about the situation.
At Dr. Yazrick's Clinic, Sweets praises Yazrick for his work on explicit memory retrieval and its ability to alter destructive behavior. Dr. Yazrick has used the techniques to quit smoking. However, now Dr. Yazrick has replaced his smoking addiction with a chewing gym habit. He explains that when he first started treating Claire, she had no memory of her past. However, they made progress and in their last session, Claire remembered parts of her wedding. Booth asks if Yazrick knows of anyone who would hurt Claire. He mentions Trevor Quan, a patient from their group sessions who became emotionally attached to her. Booth likens Trevor to a stalker.
In the Bone Room, Brennan examines the bones. Cam stops by to tell her she hasn't had any luck determining the murder weapon. Brennan discerns spider web fractures on the frontal bone. This means Claire suffered head trauma around her time of death that caused her old fractures to reopen. There are particulates in the fracture's crevice that may help find the weapon.
Booth, Sweets and Dr. Yazrick question therapy patient Trevor Quan. Trevor suffers from aphasia, a condition that prevents him from speaking unless he is playing his violin. Trevor believed that he and Claire belonged together, and that Claire was afraid of her husband. Sweets suggests that if Trevor felt Claire was moving on with her life, he might prevent her from leaving. Booth finds a tin of linseed oil in Trevor's violin case. Things aren't looking good for Trevor.
Angela breaks Cam's no babies rule by bringing Michael Vincent to visit Hodgins in the Lab. Cam walks in and is not too happy to see the baby. Hodgins tries to distract Cam by telling her Trevor's linseed oil wasn't a match for the oil found in Claire's grave. He did discover that the fibers from the grave are used in handbags and luggage. Maybe there was a bag in the grave.
Brennan and Booth meet for coffee at the Capital Grind. Brennan apologizes for their conversation at the Diner. Booth gets a call and has to go. They part, on slightly better terms.
At the FBI, Booth meets up with Sweets. He tells Sweets that Brennan couldn't figure out what caused Claire's prior injuries. Booth hands Sweets two domestic disturbance reports that were filed against Claire's husband. They're going to question the husband again - maybe he can shed some light on the subject.
Cam checks in on Wendell in the Bone Room. Wendell has discovered that Claire was shot around four months ago. The wound wasn't life threatening and pieces of the bullet are still embedded in her femur. Wendell suggests that Angela may be able to match the striations on the fragments to the gun.
Pastor Joseph Serrano explains to Booth that because of her amnesia, Claire would wake up confused and frightened. Once, she came at him with a pair of scissors. Booth notices that Karen Alford was at the house both times the police were called. Joseph explains that she is a close family friend. Booth implies she may be more than a friend, but the pastor declares he is a man of God and has a clear conscience.
Angela works through the ATF's ballistics database to find the owner of the gun used to shoot Claire. Angela asks Brennan for an update on Booth. Brennan tells her he doesn't want to live at her place and she doesn't feel comfortable buying a new place in an uncertain economy. Angela tries to assure Brennan that she and Booth can make any life they want. She doesn't have to be alone. The Angelatron beeps. They know who shot Claire.
Booth and Sweets inform Dr. Yazrick that Claire was shot during the time she was missing. She broke into a West Virginia home with a partner and the homeowner fired at them. Dr. Yazrick says her behavior could be consistent if she befriended a criminal and adopted the same persona. He agrees to check his files but he doesn't recall Claire ever mentioning the incident.
Hodgins tells Wendell that the tool that killed Claire was a Glock Feldspaten: a field spade that's used for digging and gardening. There is a 175-millimeter saw blade on one end, which could have easily been jammed through Claire's mouth and into her brain.
Booth goes to a halfway house to question Ricky Duval, Claire's crime spree partner who just got out of prison. Ricky says Claire told him her name was Brenda. Booth wonders if Ricky could have escaped to Hamilton State Park to kill Claire without anyone noticing, but Ricky has been on his best behavior. Ricky wonders if her body was found by the oak grove. Booth asks if there was a bag buried at the park. Ricky admits there was. It contained around $80,000. Did Claire go to Hamilton State Park to retrieve the money?
Sweets and Booth discuss the case over take-out food. Sweets makes a timeline of Claire's life: Claire suffers a head injury, she gets amnesia and loses contact with her husband, she finds Ricky Duvall, they go on a crime spree, Claire gets shot, Ricky gets arrested, Claire starts to remember her old life and is found wandering around D.C., she's taken to Dr. Yazrick for treatment, and is murdered and buried at the park. Booth tries to understand it all when he gets a phone call from Brennan - she needs his help.
Booth rushes to the Jeffersonian to help Brennan who has fallen and become trapped. Booth apologizes for pushing Brennan to move in with him. He only wanted his child to know that he was a good father who provided a real home. Brennan sees the benefits of their family being under one roof and accepts the offer to live together. They will find their own house. Suddenly, she notices the pictures of Claire's grave on her monitor. She realizes that the paintball splatters could be covering up evidence.
Sweets tells Booth that he has gone through Dr. Yazrick's notes twice, and none of the information implicates Claire's husband. They realize that Dr. Yazrick doesn't have any notes about Claire's lost six months. Did he remove them? Booth finds codes in the margins of the notes: "5S 1000," "TH 2500," "BJ 1500." They all have to do with gambling. Booth knows the doctor has an addiction.
Hodgins and Wendell go to the park with a portable X-ray machine to examine the paint splatters. Cam and Brennan conference with them via laptop. Brennan pulls up one of the X-rays and enlarges it. It's not sap, as Hodgins had hypothesized - it's chewing gum with an impression of a tooth, which is just as good as a fingerprint.
Booth and Sweets confront Dr. Yazrick. They subpoenaed his dental records and matched the chewing gum found at the grave. Booth tells him they know about his gambling problem, and know that his bank account was dry. Dr Yazrick defends himself. He gave Claire her life back and wasn't asking for much in return.
Back at Booth's Apartment, Booth watches sports as Brennan looks at houses for sale. Brennan wants to buy a three million dollar home, but Booth wants to split everything fifty-fifty. This won't be as easy as either of them thought but they are excited by the endless possibilities of their new life together.