At the residence of the FBI Deputy Director Ray Wynne in Alexandria, VA, Hood is waiting for him to attend an event and they're running late. Rachel is outside. Mr. Wynne's wife is getting ready in her bedroom. We see someone taking a gun from a hanging jacket as Mrs. Wynne turns around. Wynne and Hood are discussing ties when she tells him from her bedroom that she has a problem so he goes to see her. Hood calls Rachel. They're talking when they hear a gunshot coming from upstairs. Hood rushes to the bedroom and he sees a woman holding Mrs. Wynne and pointing a gun at her. The woman is very upset. She says she wants her baby back, that someone took him. Hood asks her who. She says him as she points his gun at Mr. Wynne, and Rachel appears behind her, taking her gun and cuffing her.
The woman's name is Sophia Lyons and she works for the FBI as a lab technician but she had been under special care for the last 6 weeks. Felix asks him why she came after them. Mrs. Wynne tells him that Sophia had a breakdown because her boyfriend dumped her and she lost a baby. And her husband, who was Sophia's boss, did everything to make sure she was fine.
Hood is talking to Sophia. She tells Hood her problem with Wynne is that he stole her baby.
Back to Mrs. Wynne telling Felix and Rachel that Sophia had the idea of the FBI stealing her baby and that her husband was the father.
Sophia tells Hood that she's telling the truth even when Wynne will tell lies about her. She asks him to take something out of her pocket. It's a small implant. She says that they were trying to re-program it but she ripped it off. They were drugging her against her will, but she's fighting to stay sane. She begs Hood to help her. She says that she's a scientist too and when she beats the drugs, she'll make things right. She's taken away.
Rachel meets Hood and talk about how Sophia told the police that Wynne and her were lovers and that they took her baby. He tells Rachel how some people can make things up. Then he shows her the implant. Hood says she's desperate. He also says that she's very smart, she believes every word she says, and she's very dangerous.
Hood and Rachel arrive at the Recovery Center where Sophia is being held at. She's been there for a week. Hood had the implant analyzed and it's a biodegradable device that releases a very strong anti-psychotic drug. Rachel thinks she might have been part of a clinical trial. But to be part of one, you need to give your consent and be stable, which she isn't. They see Sophia getting out of a pool. She looks very normal. She tells Hood she's embarrassed about what happened last time they saw her. She asks them to forget whatever she said or did because she wasn't herself. Hood says that if there's anything she wants to tell him she can do it. She says there isn't. That Wynne is a good man and all her troubles were cause by the boyfriend who left her. And that she never had an affair with Wynne or a baby. It was all in her head. Hood doesn't buy it. She says she doesn't need any help and walks away. Hood looks at her back and notices a new implant, somewhere she can't reach it. Hood asks Rachel to find a hairbrush from Sophia.
Hood meets Dr. Sheppard, who is in charge of Sophia's case. She's there voluntarily but only because The Wynnes didn't press charges if she completed the treatment, but if she refuses she goes to jail. Hood asks him if he's not concerned about her delusions. He says he's only worried about the chemical imbalance that causes it. Hood asks about the implant trials. Dr. Sheppard says that it can make lots of patients live a very decent life. Hood wants to know if Sophia had a problem with the implant. The doctor says the treatment is working. Hood says there could be side effects like miosis, constriction of the pupils. Rachel says that's she was covering her eyes from the sun when they were talking to her; Hood says that maybe it was because her pupils were wide open. Dr. Sheppard thanks them and leaves. Hood asks Rachel if she got it. She shows him the hairbrush.
Hood is analyzing Sophia's hair. He wants to know ho much drug there is in her system and how long she's been taking it.
Dr. Sheppard is checking Sophia's eyes. She asks him if Hood told him something. He says Dr. Hood only wants her to get better. She takes the doctor's car keys from his pocket.
Hood has finished analyzing the hair and he finds out that Sophia didn't lose her baby, but she carried him full term.
We see Sophia leaving the center. At the same time, Dr. Sheppard realizes his keys aren't in his pocket.
Hood also finds out that Sophia had been taking street drugs too, to cancel out the ones from the implant. But instead of making her better, it's making her worse. She's fighting to stay sane.
Sophia finds the doctor's car and he tries to stop her. But she gets away.
Rachel finds crystal meth and other drugs in Sophia's room. Hood asks her roommate if she knows where she is. She won't say a word. Hood tells her that she's not doing any good if she covers for her because she's delusional. She says that the whole boyfriend-dumping-her story was their idea. Hood reassures her that all they want is help her. She says that Sophia thought they were trying to take away her 'gift to fury'. And she needed it to get her baby back. She was going to catch the big man and make them give it up.
Hood and Rachel arrive at Sophia's house and they find a home made lab. She made a fire bomb. Rachel calls Felix to alert the Wynnes.
Felix is with Wynne as he's calling his wife and tells her to go to their lake house with the kids.
Hood and Rachel are driving around looking for the lake house. Hood asks Rachel to let him drive once in a while. Rachel says she let him drive once and never again. They find the house and stop. Hood gets a text message and he tells Rachel he was thinking of Sophia's boyfriend. Suddenly, the house explodes. They get out of the car and meet Mrs. Wynne and the kids. She tells Rachel that when they got to the house Sophia was there and ask them all to leave then she went away. Rachel walks away looking for her. We see Sophia hiding and looking delusional. Rachel is crossing a garden when lights go on. She keeps walking. Suddenly, she's hit in the leg with a bolt from a crossbow. Sophia did it. Rachel is in a lot of pain and screams. Hood hears her. Sophia comes to Rachel and apologize. Hood is looking for Rachel. Firemen and police officers arrive at the scene. Then Hood meets Wynne and he says that if he had pressed charges she'd been locked away. Hood confronts him saying that Sophia never miscarried and had the baby. And that the mysterious boyfriend only exists in the FBI file. Wynne doesn't want to believe it. Hood thinks someone inside the FBI created it not a high lab technician like her. He asks him if he's the baby's father. He says he's only her boss. Hood says that he has a weekend home that Sophia knows very well where it is. Hood says he thought the problem with her was the treatment but the truth that she is taking drugs to hold on to reality not her delusions. Wynne wants to hit Hood and he challenges him, but then he says he can do better than that.
Hood gets a call. He thinks it's Rachel but it's Sophia on the other line. She apologizes for having Rachel passed out on the backseat of the car. She tells him to not trust Wynne. Hood asks if Rachel is fine, if she hurt her. He tells her she almost killed the family. She tells him they weren't supposed to be there since that is the place she and Wynne met. And they made the baby there. Hood wants to know where she is but she refuses to tell him. He says he's looked in her story and that he believes her. But she doesn't care about it. Now that she has Rachel he would do what she wants. Hood wants to talk to Rachel. Sophia orders him to go to her apartment and turn on her computer. Hood tells her he would help her but she doesn't believe him. She throws the phone out the window. Hood is very angry.
At a motel room, Rachel is handcuffed to the bed and she's yelling for help. She's very desperate. But no one hears her because there's loud music coming from the next room. Sophia comes in. She's bought her some painkillers and a wi-fi phone so they can't trace the calls. Rachel tells her that she's going to jail, that they tried to help her but she blew it. She tells Rachel she can put her leg up on an pillow. Rachel say no but it's too late. Sophia has moved her leg and she's in pain. She's bleeding. Then Sophia tries to move the bolt but Rachel stops her. She tells her that if she wants to bleed to death, she'll let her know.
Back at the lake house, Felix tells Wynne that they couldn't find Rachel. And they got no answer in her phone. Wynne orders other agents to find her. The FBI Director arrives. He tells Wynne that they're doing everything to protect his family until the woman is caught. Wynne tells him they have a problem. Jacob Hood. He provoked the situation and he has endangered Rachel's life. The Director doesn't believe him. Wynne tells him that if he will keep thinking that once an agent is dead. The Director asks Felix for Hood, but he has no clue.
Hood is at Sophia's house and he's thoughtful about the whole situation. Then he sees an incoming call on the computer. It's Sophia. Hood wants to talk to Rachel. Sophia tells him that Wynne and her were lovers and she didn't plan to get pregnant. He wanted her to get an abortion but she didn't want to. Then the plan was to give the baby up for adoption and then is when the boyfriend story came up, to protect Wynne. But when the baby was born, she changed her mind, but Wynne wasn't happy. And then she doesn't remember. She thinks she must've been drugged. Then she woke up 36 hours later without her baby. Hood asks her what she wants from him. She wants her baby. Hood asks her to meet him so they can work it out. She just wants him to find her baby, then she will give him Rachel and she will disappear. She says that if that doesn't happen, someone will die. As she ends the call, a picture appears on the screen. It's Rachel's, cuffed to the bed.
Back at the motel, Rachel is clearly in pain. Sophia looks worried and she offers Rachel some painkillers but she refuses. Sophia says that when she gets her baby it will be a new start for her. Rachel says she's expecting too much from him. She says Hood is a genius and a good man, but he's not practical, so she should let her make a few calls. Sophia doesn't buy it. Then Rachel asks her if she really had Wynne's baby. She says she had a boy. And she won't give her his name because she will have to change it when they leave. Rachel asks her if she really thinks that will happen. She hopes so. For Rachel's sake.
Wynne goes to the Director's office and gives him Rachel's phone. He tells him that the last call was made to Hood, right after Rachel went missing. The Director wants to know what's the point. Wynne says why Hood didn't report it, instead he went after her. The Director asks him if he wouldn't go after his partner. Wynne tells him Hood is complicit, but the Director doesn't think so. Wynne says that he knows Hood and he are friends but Sophia was doing fine until Hood visited her at the Recovery Center and then the things that happened. Then Hood gets in contact with her and disappears. He wants an explanation to all because his family is in danger.
Felix gets a phone call. It's Hood. He's calling from a pay phone because he doesn't want to be traced. He's found a way to track the baby's whereabouts and he needs his help. Felix is shocked. Then, Wynne comes out to talk to a group of agents and tells them that he just spoke to the Director and Hood is now a 'person of interest' in the shooting and kidnapping of Agent Young. Hood is listening to all. He tells them he's a civilian, not an agent. So he wants the man who betrayed her pay for it. Hood hangs up.
Felix meets Hood at a cyber cafe. He tells Felix that Rachel is hurt and that he needs to give her the baby so they can have Rachel back. Felix wants Hood to go back with him to the Bureau. But Hood tells him they're looking for Rachel, but also looking for him and if he wants to leave he won't hold it against him. Felix stays. Hood is looking at Maya's myspace page, Wynne's daughter. He then notices that both Wynne's and his son's eyes are kind of yellow. It's a condition called Gilbert's syndrome. It only affects males. So there's a chance Sophia's baby might have it. Felix says that if there really is a baby he can't be serious about giving it back to her. Hood says he might be right but Sophia didn't ask for what's happening to her.
Back at the motel, Sophia is taking more drugs in the bathroom and Rachel tries to get the phone from a table. Sophia catches but all she does is tell her that it's important if Hood calls.
Felix gets to the NIH to find out about any child who's being treated for Gilbert's syndrome . He lies to get the receptionist give him information. He asks her to see if they have any 6 month old child on the database. There's a result. But the baby is not with his birth family, he's in foster care pending adoption. Then he gets to take a look at the screen. Then he says it was just a waste of time and leaves. Felix tells Hood about this. He asks what's the next step. Hood says it now gets tricky.
The phone rings at the motel. Hood tells Sophia that he wants her to meet him. He asks if Rachel is listening. She is. But so is the FBI. Hood gives her an address, and tells Sophia it's a diner where Rachel and he had the worst pancakes. He hangs up. Sophia gets ready to leave but Rachel tells her that it is a false address, because the FBI must be listening, but she can tell her where the diner is.
The FBI arrive at the address. There's nothing there.
Rachel and Sophia arrive at the diner. The place looks abandoned. Rachel says it was the pancakes. They probably poisoned someone. They enter the place and Hood comes to Rachel and holds her. He helps her sit down. Sophia asks where her son is. Hood says it's here and takes out his cell phone. Rachel looks like she will pass out and Hood sits behind her to hold her steady. He makes a call and Felix answers. Sophia is not happy about it. Felix says that he's looking at the couple who's taking care of her son and Hood shows him the live video on his cell phone. She takes it from him and sees the video. Hood is worried about Rachel and begs her to stay awake. Sophia is very touched watching her son. At the FBI, they've located Hood's position. Sophia is very angry now, she says that doesn't help her. He just tried to buy some time to keep her away from her son. Hood asks her to look at him. He says the baby is fine with those people and he wants her to keep him that way until they sort things out. But Sophia won't listen, she wants the baby with her. Hood is very angry now and tells her to think about what's best for her son. Sophia tells Hood that that wasn't the deal, that she could trust him. Hood says she can but they have to get Rachel to a hospital or she will die so he orders her to give him his phone. Sophia is upset and before she leaves she pulls the bolt out of Rachel's leg to Hood's horror and Rachel screams in pain as she starts bleeding profusely. Sophia takes the car and Hood's phone. Hood desperately looks for something to stop the bleeding and then he goes outside and sees an old truck. He goes back inside and carries Rachel into the truck. She's tired but he tells her to stay awake. Rachel is in very bad shape and Hood tells her they will work it out. She tells him that if it doesn't, it's not his fault because he can't fix everything.
Hood and Rachel arrive at the ER. He carries her inside and watch the doctors work on her. He looks very stressed.
A few hours later, Hood is sitting on a chair when Wynne stands in front of him. He tells Hood he's caused him a lot of trouble. Hood says he hasn't even started. Felix and the Director walk in. Hood tells him that he knew he had some surveillance on his phone so Felix shows him the video of the baby and the couple in a park. Hood says the DNA test will confirm that he's the father. It's all over. And so is he.
Sophia is a the park and she has spotted the couple and her son. She approaches the woman as she's playing with her son. She asks if she can come closer. His name is Michael. She's very emotional. Felix comes and asks her to come with him. She stands up and says good-bye to her son.
Rachel's doctor tells Hood that she will be fine. Hood walks into Rachel's room and she's feeling fine. She will start physical therapy the next day. She asks about the case. Hood tells him that Wynne is being held without bail and Felix went for Sophia. Rachel tells him that he can tell his new handler not to get too comfortable since she'll be out of there soon. Hood says he's decided that if she wants to transfer out, he won't stop her. Rachel thinks it's a joke. He tells her that she's lucky she's alive and if it had been the other way around, he would've been able to deal with it. Rachel tells him that she does not want another assignment, that maybe her classmates at Quantico are ahead of her and she barely remembers her apartment but if it was someone else on that bed, she would be jealous as hell. Hood smiles and can't believe it. Then Rachel says that he needs her anyway, because he's the worst driver in the world.