Caroline Julian barks at the head of the Parole Board, Harriet Grover, not to let hacktivist Christopher Pelant walk free. Harriet tells Caroline to shut up and sit down. Caroline joins silent Booth and Brennan. Pelant's lawyer, Meg Vinnicombe, explains to the board that her client has lived within the guidelines of his sentence and that the FBI has done nothing but harass her client. Pelant apologizes for his past behavior, claiming he is a changed man. Booth doesn't buy it and interjects, telling Harriet that Pelant is still a suspect in two murder investigations. This is news to Harriet. Brennan presents her with files containing information about the case. Harriet looks at the horrific pictures of the dead bodies. With the new information, Harriet denies Pelant's parole until the board can analyze the files. Suddenly, a wolf's howl fills the room. It coming from Booth and Brennan's cell phones-the ringtone has been changed.
Later that night, Booth and Brennan join Cam at a crime scene in the woods. Cam explains that a couple on an ATV found the remains. Booth gets a text message from the priest performing Christine's baptism-everything's all set. Brennan is supportive of Booth's decision to have their daughter baptized but doesn't plan on attending. The gang meets Hodgins, who is examining the body. The victim is male, in his late 30's with little tissue left. Brennan notes that the dentition on the bones is from a pack of wolves. She also notices a remodeled break that is 28mm long on the medial epicondyle and the trochlea. Hodgins places time of death around two days ago, based on Piophilidae eggs on the body. Hodgins notes that the victim was wearing scrubs. Brennan realizes that she was the one who set the break. Pelant killed her friend!
At the FBI, Booth and Sweets talk about the victim, Ethan Sawyer, who was a delusional schizophrenic in a mental hospital. He is missing from the hospital but hasn't been officially identified as the victim. Booth tells Sweets it is Ethan's body, because Brennan recognizes the elbow break. Sweets tells Booth not to jump to any conclusions that the murderer is Pelant.
Wendell and Cam examine the body on the platform. Wendell notes that around five to six animals ingested seventy pounds of soft tissue. Wendell is in awe of Ethan's accomplishments, which included specializing in artificial intelligences as well as human behaviors. Cam notices hemorrhagic staining on more than fifty percent of the bite marks, meaning that Ethan was still alive with the wolves started to eat him. Cam immediately calls Brennan with the news. Brennan believes that Ethan was drugged or paralyzed so the wolves believed him to be dead.
Brennan is shaken up by her friend's grisly murder. She makes a confession to Booth. She had been conferring with Ethan on the Pelant case. Booth is upset at Brennan for putting the case in jeopardy. Brennan apologizes. Booth tells Brennan he won't tell Caroline and that sometimes you have to work outside the system for the greater good.
Booth and Brennan arrive at the Psychiatric Hospital and watch a video of Ethan being questioned by his doctor. Ethan is erratic and tells the doctor that he needs to dispatch a demon, that looks like a baby. Booth is surprised to learn the "demon" is Christine. Brennan tells Booth that Ethan never threatened their daughter directly. The last time she visited him was around two weeks ago. The couple talks to Dr. Alyson Noble, who explains that Ethan had escaped about a year ago. She tells them that this time Ethan was accidentally transferred to an open ward due to a computer glitch. Brennan tells Booth the last time she saw Ethan, he gave her an old mathematics book as a gift. Booth tells Dr. Alyson Noble he will need all the visitor logs and security footage.
Hodgins checks in with Wendell. Hodgins has a theory that Pelant fooled his ankle bracelet into thinking he was at home. Then he drugged and lured Ethan out of the hospital, and left him in the woods for the wolves. Wendell tells Hodgins he is going to follow Brennan's rules, which means to gather evidence and follow it without bias.
Angela watches the security footage from the hospital and finds something startling. She brings her laptop into Brennan's office to show her. It's footage of Brennan leaving the hospital and it is time stamped the night before Ethan Sawyer disappeared. Brennan says this is an error and that Pelant must have hacked into the security system. Angela tells Brennan that she needs an alibi but Brennan doesn't have one. Angela lies and tells her they were at the Founding Fathers bar together having a drink. Angela tells Brennan that she would have motive for murder if someone was threatening to kill her daughter. Brennan realizes Pelant is framing her for murder...
Booth and Brennan try to comprehend what is happening to Brennan. The footage clearly states Brennan left at 7:14, giving four hours unaccounted for. Max walks in to hear the couple arguing. He offers his help but Booth tells him they have it under control.
Cam finds a puncture on the C7 vertebrae that Brennan missed in her notes. Wendell brings up the X-rays to show the puncture. It seems to be the tip of a needle. Cam grabs the rotary saw to reveal the tip of a hypodermic needle. Cam pulls out the tip and gives it to Wendell to pass onto Hodgins for analysis.
Booth and Brennan get ready for bed. The couple decides not to change anything in their lives due to the new developments. Brennan still will not attend Christine's baptism, and Booth tells her he appreciates and loves her just the way she is.
Pelant tears apart an old digital clock radio. He's doing something with the wires and coils within the clock. He's up to no good again.
Brennan arrives early at the lab to examine her friend's bones. Brennan shows Wendell a cut mark on the victim's temporal bone. Brennan decides that since she missed seeing the needle puncture she will examine the bones herself so she doesn't miss anything again. Wendell leaves her to her work.
Hodgins explains to Cam, Angela, Wendell, and Sweets that the needle tip had curare on it. Curare was used as anesthesia in the 40s. It leaves the body quickly, which is why it didn't show up on the tox screen. The group wonders where you can get a drug like that today. Hodgins explains that it comes from the plant Chondrodendron tomentosum, which he had in his Ookey Room. However, two weeks ago Brennan asked to have one of the plants. The group takes this in and tries to be objective in dealing with the new revelation. Angela freaks out at the rest of the group for even considering Brennan as a suspect instead of Pelant!
Angela rushes to the FBI to find Booth. She explains the evidence is piling up against Brennan. Booth tells her that she needs to figure out how Pelant put Brennan on the security video. Booth gets a phone call from a frantic Brennan. Pelant's got her and she's locked in his house!
Booth rushes to Pelant's home but finds no sign of Brennan. Booth beats up Pelant and throws him around the room. Pelant breaks his ankle monitor, forcing the police to come. Pelant tells Booth to call Brennan, who is safely at home.
Caroline scolds Booth for his behavior. There is no record of the phone call from Brennan, Booth tries to explain that Pelant did it. Caroline informs Booth that Pelant's lawyer went to the parole board after he was attacked and they let him go. Booth and Brennan are officially off the case. Special Agent Hayes Flynn will be taking over. Booth decides he will take his suspension at home in case Pelant decides to drop by.
At the Angelatron, Angela, Cam and Wendell look at the work Brennan did before she was removed from the case. There are cuts on all the minor arteries. The wolves were drawn to the victim because of the smell of blood. Cam leaves Angela's office to report this to Agent Flynn. Angela is furious.
Angela rushes over to Booth and Brennan's house, ignoring Cam's request not to contact Brennan. Angela demands all of Brennan's passwords so that she can look into the email exchanges between Brennan and Ethan.
Agent Flynn asks Sweets about his profile of the murderer. Flynn asks if his profile could be applied to Brennan. Caroline tells Sweets he has to answer truthfully. Sweets tells Flynn it could be applied to Brennan, but she is a good person and didn't do it. Flynn can sense that Sweets is too close to Brennan to view this objectively and informs him that he will be taken off the case.
Back at the house, Angela shows Booth and Brennan her findings. She was able to hack into Pelant's credit card, phone bill, and library card. He had over eighty books delivered in the past three months and ordered just as many pay per view movies. Suddenly there is a knock at the door. Angela hides herself. It's Agent Flynn. He has a warrant to search the house and Brennan's Prius. Booth informs Flynn that the address on the warrant is incorrect so he has to come back. Flynn is annoyed but tells Booth that he is going to search the Prius. After Flynn leaves, Booth orders Angela to get to the library and figure out why Pelant checked out those books.
Hodgins walks into the Autopsy Room to find Cam crying at her computer. The results from Brennan's Prius - Ethan's hair was found in the trunk. Hodgins is devastated. Cam tells him that after she pulls herself together she's going to report it. She believes in the system.
Caroline visits Booth and Brennan at home. She has no choice but to put out an arrest warrant out for Brennan. Booth is devastated but Brennan thanks Caroline for the courtesy call. Brennan hears Christine cry and she goes to her.
Hodgins checks in with Angela, who is knee deep in books. She can't find a pattern or solution as to why Pelant wanted these books. Even though Angela is frustrated, she appreciates the support from Hodgins.
Brennan and Booth watch Christine sleep peacefully. Suddenly, Max pops his head into the nursery: we need to talk. Max tells Brennan she needs to make a run for it, but Booth says that will only make her seem guilty. Max tells them that computers are the system, and once you're in the system, they'll never let Brennan go. Max leaves, frustrated that no one will listen to him.
Brennan tells Booth that she wants Christine baptized before she is arrested. Brennan grabs a math book Ethan gave to her. He left a quote in the book from Alexander Pope: "Nature and nature's laws lay his in night; God said ‘Let Newton be' and all was light." Brennan realizes that Ethan was sending her a message about math and light in quote. They need Hodgins to go to Ethan's room at the hospital.
Cam and Hodgins go to Ethan's room. Hodgins tells Cam that Brennan said the message would be written within a triangle, however, patients aren't allowed anything sharper than their fingers in their rooms. Cam grabs the ALS light and shines it on the walls. She sees odd lines on the wall. There is an illuminated code within a triangle on the wall. Cam touches a phadebas press test paper to the wall and sprays. Cam realizes Ethan left the message in his saliva!
Brennan is at church while she and Angela discuss what the code could represent. Angela wonders where books and computers cross. Brennan thanks Angela for her support and help. Brennan joins Max and Booth at the church altar for Christine's baptism. As Max ducks out of the church, he mysteriously tells Brennan to think only of her family.
Brennan and Booth proudly watch as their daughter is baptized. Meanwhile, back at Booth and Brennan's house, Pelant walks in the front door. He makes his way to Booth and Brennan's bedroom and replaces their alarm clock with the alarm clock he was working on. Back at the lab, Angela starts to scan the library book, which suddenly scans a code onto her computer.
Angela goes to Caroline, who is in the FBI Lobby. Angela explains how Pelant added mini programs into the library books. The programs were uploaded when the books were scanned. Caroline tells her that her theory isn't enough to arrest Pelant. She reveals someone made it look like Caroline was transferring money into Brennan's account. Caroline is off the case as well. Angela is angry at the situation and especially at Cam for reporting everything to the FBI. Caroline tells Angela that is because of Cam that the Jeffersonian squints are still on the case, which is what Pelant fears the most. Cam is actually the hero, not the villain.
Booth and Brennan leave the church. Booth goes to get the car. Brennan tells him she loves him and that Christine is not the only reason why they are together. Booth tells her that he loves her and continues to the car. Once Booth is gone, Max pulls up. Brennan puts Christine in a car seat in the back. Max advises Brennan to drive as far as she can without getting tired. No stops at chain restaurants or motels and always pay in cash. Brennan knows what she has to do and knows her father is right. Max tells her to wait for him where they said and if he's not there in three days, to move on to the next place.
Brennan hugs and kisses her father goodbye and drives away. Booth is at his car, which won't start when he sees Brennan drive away. He runs and shouts for her but she's gone. Booth is enraged and Max tells him this is the way it has to be. If Booth knew where they were going, he'd be an accomplice, so he has to stay in the system and bring his family home. Max promises to keep his family safe.
Booth sits alone on the church steps as Brennan and Christine drive into the unknown.