In an alleyway, a cop finds the bloody body of a young girl next to a large kitchen knife. Is she dead? He nudges her and she opens her eyes! She picks up the knife and stabs the air in front of her, wailing while she fends off the officer.
Booth and Brennan discuss baby gifts for Angela and Hodgins at the Diner. Caroline Julian enters, insisting Brennan go to the Lab. They have a case. She needs Brennan to examine a living girl to discover if she is a murderer and who her victim might be. They can't question her because she is a deaf-mute.
On the Forensic Platform, Brennan and Caroline Julian approach Grace Meacham and Jane Doe, who is still covered in blood. Grace has been assigned by Child Protective Services to represent Jane. Brennan states that they don't yet know if Jane is a child. Cam confirms that Jane is covered in another person's blood. She was wielding a large knife and had bloody money on her person. This could be a robbery that went bad. If they determine who Jane Doe is, they may be able to save the person she stabbed. Grace signs to Jane that Cam and Brennan will begin their testing. Jane makes a break for it, trying to run away. Brennan and a Security Guard restrain the girl as the alarms blare.
Hodgins tries to collect particulates from Jane Doe as she struggles. She has no intention of cooperating. Arastoo is uncomfortable causing Jane Doe such anguish. Grace explains to Jane that they need to do dental X-rays to establish her age and locate her parents. It is likely that she has family somewhere as no foster children were reported missing. Jane becomes even more distressed at the mention of her family.
Hodgins and Angela discuss Jane Doe. Angela can't believe how sweet and innocent their potential murderer looks. She can't believe that a baby could grow up to become that person. Speaking of which, she can't wait to hold her own child. Soon enough.
At the FBI, Caroline reports there are no stabbing victims in the hospitals and morgues. Booth may have a lead. They found $78 on Jane Doe, along with a crumpled ball of paper that Angela will reconstruct. The money all has sequential serial numbers. It came from an ATM. They can trace the numbers to a specific ATM and potentially find the victim.
On the Forensic Platform, Arastoo struggles to get dental X-rays from Jane Doe. She won't open her mouth. Brennan threatens to have Jane Doe sedated so they can obtain the information they need. Sweets arrives and pulls Brennan aside. Jane Doe is terrified, disabled and restrained by strangers. He suggests that Brennan make sure Jane feels comfortable and secure. He reminds Brennan of her time in foster care and how frightening her experiences were. Sweets never wanted to cooperate and he is sure Brennan didn't either. Jane Doe bites Arastoo so Brennan changes her tactics.
In Angela's Office, Brennan attempts to use a Digital Motion X-ray Machine. It is completely non-invasive and all Jane must do is slip her arm inside. Brennan needs to see the epiphyses of the distal radius and ulna. Nevertheless, Sweets and Arastoo must force Jane to put her arm into the machine. Brennan gets what she needs: Jane is over thirteen years old but less than seventeen years old.
At the FBI, Booth tells Brennan that there have still been no reports of a missing minor matching Jane's description. Brennan is affected. She doesn't want Jane to remain anonymous. Booth has been looking into the hundreds of people who used the ATM at a bodega in Columbia Heights. Cam calls with information about the victim: he was a white male in his forties. Booth instructs an agent to call up all the photographs of white men at the ATM. There is only one white male in his forties: Duval Price.
Booth finds the door to Duval Price's apartment broken open. He and Brennan follow blood to the kitchen. Duval Price lies in a giant pool of his own blood. He is dead.
At the Diner, Sweets doesn't understand why Jane Doe would murder someone and take the weapon with her. He attacks Brennan because motive is not important to her. Brennan corrects Sweets: she intends to discover the motive whether Jane reveals it or not. How could Jane have broken that thick oak door? Why would she target a man twice her size? Sweets apologizes as Brennan has an epiphany. Sweets questioned Jane Doe and she signed during the interview. Brennan needs to see that tape.
In Angela's Office, Angela and Brennan watch the footage of Jane signing. Brennan asks Angela to play it on a loop. The way Jane Doe signs is just like a dialect. Using videos from the Linguistics Department, Angela determines that Jane Doe is from a rural town in Southern Pennsylvania.
At the FBI, Booth shows Caroline Julian the reconstructed piece of paper. There is handwriting on the paper: Bus 122. It is the only bus that arrives in D.C. from Crossroads, Pennsylvania. The paper is also a receipt from a hardware store. Luckily, there is only one hardware store in Crossroads, PA.
Booth enters Shenfield Hardware. He shows Jane Doe's picture to Mike and Denise Shenfield. They recognize her: that is Amy, their daughter.
Booth wonders why Mike and Denise didn't report their daughter missing. They explain that Amy has run away before but she always comes back. She is an unruly child and they couldn't handle her. She would kick and fight but she always came back when she ran away and said she was sorry. They can't believe she has killed a man. Booth agrees to let the Shenfields see Amy.
At the Lab, Hodgins examines the oak door from the victim's apartment. It was too thick for Jane to break down. She would have suffered severe injuries, none of which were evident on her body. Hodgins also found fibers on the splinters in the door. They don't match Jane's clothing. They need to determine when this door was broken.
Angela explains to Hodgins that she had Braxton-Hicks contractions but she is fine. She didn't want to worry him. Hodgins wants to be there for her. He went through the birthing classes. He can handle this. Speaking of water breaking, Hodgins realizes he can analyze the moisture content in the door to determine when it was broken.
Arastoo joins Brennan in the Bone Room. She instructs him to look at Jane Doe's X-ray. Arastoo notes that Brennan is becoming personally invested in the case. She is offended that he thinks her objectivity means she doesn't care. If she knew how to convey her emotions she would, if only to make his life easier. She points to the X-ray. It shows signs of child abuse.
Brennan sits with Grace and Amy. Brennan wants a full set of X-rays. She needs cooperation. Brennan mentions that Amy suffered child abuse. Amy is surprised. No one has ever believed her before. Brennan tells Amy that her bones will not lie. They will tell the truth about what happened to her. No one will be able to dispute the facts. Amy agrees to give the X-rays.
In the Bone Room, Arastoo and Cam look at the X-rays. Amy has been severely abused for years. It is clear why Amy didn't want them to contact her parents.
Brennan and Booth wait for Caroline Julian at the FBI while Mike and Denise Shenfield sit in the Conference Room. Mike gets impatient when Caroline and Grace arrive. Caroline has a court order preventing the Shenfields from seeing Amy. They have been beating her since she was three years old. Brennan wonders why. Was it because she couldn't hear? Amy has Wardenburg's Syndrome. She got it from one of her parents. Why didn't they understand? Brennan has a sudden realization. She approaches Mike and Denise, feeling the bones at the tops of their noses. Brennan tells Booth that they don't have high nasal roots. These are not Amy's biological parents.
rIn the Interrogation Room, Booth presents the Shenfields with a copy of the fake birth certificate they were using to prove Amy was their daughter. Sweets wonders where they got Amy. She was never beaten until age three, meaning she was safe until then. Mike tells his wife not to talk but she starts to break when Sweets pretends to understand. Mike takes matters into his own hands, slapping his wife. Booth grabs Mike and punches him.
Brennan and Arastoo examine the bones of Duval Price. There is a nick on the inside of the manubrium, which doesn't make sense to Brennan. She determines that Amy and Price must have been face to face. Price knocked Amy down and fell on top of her. She stabbed him in the back over his shoulder. Amy was defending herself.
Hodgins explains to Angela that according to the moisture in the door, it was broken open at 2AM. Cam put Price's time of death at midnight. The door was broken open two hours after the murder. Someone else knocked it down, saw Price dead and left him there. Angela starts having contractions. Hodgins panics. He doesn't know what to do, other than scream BABY! Angela tells him to get the car but he can't find the keys.
At the FBI, Booth tells Caroline that they found a notepad in Price's apartment that said 122 and 11:55. It signifies the bus Amy took and the time she arrived in D.C. According to phone records, Mike Shenfield called Price an hour after the bus left Crossroads, PA.
Brennan tells Amy that they know what happened. She ran away because she couldn't bear the abuse. Price kidnapped her when she got off the bus and took her to his apartment. He said that Mike Shenfield was going to come. Amy admits that Price was going to tie her up and hit her. She tried to get away. She grabbed the knife to scare him but he grabbed her and they fell. She is terribly sorry that she killed a man.
Meanwhile, Booth confronts the Shenfields. They couldn't risk Amy saying anything about the abuse so they called their friend Price and told him to apprehend Amy. When Mike arrived in D.C., he found Price dead in the kitchen and he left him there. This wasn't Amy's fault. However, the Shenfields still won't tell Booth how they got Amy or where she came from.
Brennan tells Amy that the Shenfields aren't her parents. Brennan will help her figure out who she is.
Sweets and Brennan encourage Amy to remember something from her past. It is difficult but Amy remembers one thing: a stuffed bunny. She slept with it all the time. But Amy doesn't remember anything else. Brennan has another idea. She can use one of Amy's wisdom teeth to determine where she grew up. Amy readily agrees.
Brennan and Arastoo work with the tooth until they discover that Amy came from Los Angeles. Booth uses the Missing Children's Database to locate a child matching Amy's description. She is holding a stuffed bunny in her missing photo. They found her.
Hodgins and Angela sit in the car after a disastrous trip to the hospital. They both panicked and Angela wasn't even in labor. Now they have had a dry run and they will definitely be ready next time.
Amy, whose real name is Samantha Winslow, waits with Grace, Booth and Brennan for her biological parents. Samantha is worried. Will they like her? Brennan assures her everything will be fine. Hugh and Celia Winslow arrive. They are awed by the sight of their daughter. They never gave up hope. Celia produces Samantha's stuffed bunny. Samantha runs to her parents and they all embrace.
Brennan and Booth walk together in the Jeffersonian Gardens. Brennan has decided a stuffed animal would be a nice gift for Angela and Hodgins. Booth is concerned about the fact that he slugged Mike Shenfield. He doesn't want to lose his temper. He has seen what happens when parents let anger get the best of them. He doesn't want Parker to see that side of him. Brennan insists that Parker is lucky but Booth wants this one to be about more than just luck.