A blonde Brennan sits in an open field with baby Christine showing her daughter pictures of Booth. Max joins the girls and they gather their belongings up to move to their next location.
Angela works hard in her office to try and decode Ethan Sawyer's triangle. Hodgins comes in to her office to try and urge his wife to focus on other things than Pelant, but getting Brennan back to the Jeffersonian is more important than anything.
Booth works hard at a desk in the FBI bullpen. Agent Hayes Flynn asks if he has had any contact with Brennan. A frustrated Booth tells him that he has no idea where she is. Flynn tells Booth he still has to follow procedure and check all of Booth's phone calls, emails, etc. Booth ignores Flynn and gets up to go take his lunch break. Flynn notices a Post-It note on Booth's desk: Pelant--Brookside Shelter.
Clark sits at his new desk in Brennan's old office. Angela comes to the doorway but refuses to enter the office until Brennan is back. Clark scolds Angela for not putting her report on the latest victim in the binder: Clark has started using the binder system to organize all the information on the cases. However, Angela sees no point in Clark's new ways since Brennan never used binders. Upon hearing the two bicker, Cam comes over. Cam tells Angela that she needs to listen to Clark as long as she wants to stay and use the Jeffersonian resources to try and decode Pelant's work.
On the side of the road, Max urges Brennan not to go out on her own. Brennan won't listen to her father and tells him that this is the only way and that she will be back soon. Max doesn't like it.
At the Brookside Outreach Center, Pelant helps teach a group of homeless men how to use a spreadsheet on the computer. Booth walks in and tells the administrator that he would like to volunteer at the shelter as well. Pelant and Booth see each other. Booth smiles. Pelant picks up his phone and dials Agent Flynn.
Cam and Flynn head out to a crime scene in the woods. Flynn tells Cam that they got an anonymous tip from a disguised caller with the information on the body. When the two reach the body, it has already been excavated. Hodgins tells them they have only been here for ten minutes. Clark notes the meticulous work that has been done to uncover the remains. Angela takes pictures of the body and notices a snowdrop flower leaning on a nearby tree. Angela tells the group that Brennan left the flower for them. Agent Flynn yells to the other FBI agents to search the area--Brennan's been here!
Hodgins tells the gang about the snowdrop on the lab platform. Angela tells them that it's a symbol of hope. Clark examines the remains: Caucasian female in her mid-30's. Cam tells Clark to email Booth all the information about the case, including the snowdrop. Everyone is confused regarding her instructions since they have been told to avoid emails with Booth involving Pelant. Cam tells them that there is no evidence Pelant is involved.
At the FBI, Angela tells Booth that Brennan sent a message to "have hope." Booth wants to know how the girls are communicating, but Angela won't tell him. Booth is frustrated with her and the situation. Booth gets an email on his phone from Clark. The remains belong to Carole Morrisey, a guidance counselor that went missing ten years ago.
Brennan and Max watch the news in their motel hideout. The reporter talks about the anonymous tip on the remains. The two can see the Jeffersonian team at the scene doing their work. Brennan is disappointed that Booth isn't there, but Max assures her that this is what she wanted to happen.
Over at the shelter, Pelant sees the report on the television. He grabs the remote and freeze frames on Angela with the snowdrop.
Booth drives in a beat up car. He calls Cam. He informs her that Carole Morrisey used to be a guidance counselor at Pelant's high school. Booth lies to Cam about where he is going and what he is going to do so that if Flynn asks, Cam doesn't have to lie.
Back at the shelter, Pelant hacks into the FBI server. He gets his hands on Clark's email to Booth and sees the photos of the body and the picture of Carole Morrisey. Pelant's fury grows.
Sweets gets cornered in the FBI hallway by Agent Flynn. Sweets tells Flynn that he doesn't know where Booth is and that Booth won't call him because Booth doesn't want Sweets to lie to anyone. Flynn is annoyed with everyone being so smart around here.
Booth sits in a run-down motel. He notices movement outside and grabs his gun. Someone opens the door. Booth grabs their arm and yanks them forward. The assailant disarms Booth and throws him to the ground--it's Brennan! The couple take each other in...and then kiss.
Booth and Brennan catch up with each other. Booth feeds Christine breakfast. Brennan tells Booth that she and Max were doing a lot of research on Pelant when they found out about the guidance counselor's disappearance. Brennan knew the local trails since the teacher was a runner. Brennan tells Booth that examining the photos aren't enough--she needs to see the bones. Max comes to the motel room. He tells them that he's packing up and it's time to leave.
At the lab, Cam and Clark examine the bones. There is damage to the victim's skull, which leads them to believe the victim was running away. Hodgins comes to the platform to tell them that the injuries on the skull were swabbed and contained traces of a rock: red agate. However, the murder weapon isn't a rock. The trio is stumped.
Angela and Caroline have breakfast at the diner. Angela tells Caroline that she can prove that her and Brennan's signature were forged so that Caroline can be cleared to get back to work. However, Angela has no proof that Pelant was the one that forged it. Caroline is grateful and ready to get back to work.
Outside in the woods near Brennan's hideout, she tries to examine the photos of the remains. She gets frustrated and tells Booth that she needs to see the bones and doesn't want to live like this anymore.
In the FBI Conference Room, Sweets shows Caroline some samples of Pelant's writing: essays, papers, etc. He pulls up a letter of recommendation written by Carole Morrisey for Pelant, however, the linguistics and language patterns don't match to other recommendations she wrote. The recommendation for Pelant was the last recommendation the teacher wrote before her disappearance.
Angela shows Hodgins cut marks on the victim's throat on the Angelatron. She tells Hodgins to have Clark check them again. Angela asks Hodgins to do her a favor. She needs him to go put flowers on a certain place for her. Hodgins wonders about Angela and Brennan's code but Angela won't give any details.
Hodgins walks around a local cemetery carrying flowers. Suddenly, Pelant comes to face Hodgins. Hodgins threatens to kill Pelant if he comes anywhere near the Jeffersonian team. Pelant doesn't believe Hodgins' empty threat. Hodgins throws the flowers down and strangles Pelant until he passes out.
Agent Flynn interrogates Angela and Hodgins about the flower code while Caroline and Sweets listen. Hodgins tells Flynn that he saw Pelant at the cemetery but didn't interact with him. Angela said that she and Brennan have this code with the flowers. Flynn tells Angela to go to the next grave and tell her to surrender, but Sweets tells him that now that Pelant knows the code, she won't go.
At the cemetery, Max looks around for the flowers. He calls out to Pelant that he's not going to lead him back to her. Pelant listens in the distance.
Hodgins pulls Sweets aside and tells him that he strangled Pelant. Sweets is concerned with the fact that Hodgins is capable of murder. However, Hodgins tells him that he believes Pelant is suicidal and wanted him to kill him. Sweets thinks that Pelant wanted Hodgins to kill him, which is valuable information.
Clark shows Cam the deep cuts on the victim's throat. Clark says that if her throat was slit it would have to be done by a weapon heavier than a knife due to the weapon marks and Pelant's size. Cam is happy with these finding and apologizes to Clark. She never realized that their work to clear Brennan would put Clark out of a job and she is happy that he still does a good job anyway.
Brennan and Booth worry about Max, who isn't back from his run. Brennan tells Booth that her instructions have always been that if someone wasn't back in six hours to leave and move on. Brennan apologizes to Booth for leaving and going on the run, but it is what she had to do.
At the shelter, Pelant scans through DMV records. One for Clark Edison pops up on the screen. Pelant says that Booth should have stolen the car instead.
Booth goes outside to see Max taking his beater car. Max tells Booth he saw Pelant at the graveyard and that since Booth bought the car with cash under a fake name, Pelant can still find them. Max says when he traces the car and Pelant finds him, he's going to kill him...and he's off into the night.
Booth calls Agent Flynn and tells him that Brennan is on the run in a beat up car on State Road 47. Flynn tells Booth he is the second person to call the car stolen. Booth realizes what's happening, tosses his cell phone and goes to get Brennan.
Hodgins comes into the Autopsy Room to tell Cam that she needs to leave -- as well as Clark and all the security guards. Cam realizes what is going on and leaves the Jeffersonian with everyone. Hodgins and Angela wait until the lab is empty and let Booth and Brennan enter. The gang has a happy reunion.
On the Platform, Brennan gets right to work and has Hodgins swab some of the injuries. She notes that Clark's binders indicate the weapon was an axe. Hodgins hopes that he can find something to narrow it down. Sweets steps onto the Platform. He is happy to see Brennan, but isn't comfortable with her here. Booth tells Sweets he needed someone here that can use a gun to protect Brennan.
Booth goes to Agent Flynn to tell him that Pelant violated his parole by hacking into the FBI wire wall to look at emails. Booth convinces Flynn to call the FBI computer forensics to confirm that Pelant did hack in.
Brennan examines the victim's cartilage. She realizes that Pelant snared the victim when she was running in the woods, causing her to hit her head on the red agate rock, and the wound retracted because she was being pulled up. Sweets and Hodgins are happy Brennan is back in the lab...but they still need the murder weapon.
Agent Flynn and Booth storm into the shelter and arrest Pelant for violating his parole and hacking into the FBI system.
Cam comes into the lab early Sunday morning. Hodgins tells her that Pelant was arrested for hacking into the FBI, which Hodgins realizes she knew would happen if Clark emailed Booth. He also tells her that he found Japanese steel in the bone, which will help them find a murder weapon. Hodgins tells Cam to not have the security guards come in, since he will be in all day keeping an eye on the lab.
Brennan and Angela analyze Ethan Sawyer's triangle. Sweets comes in to tell them that Pelant wouldn't have killed Ethan if that code didn't scare him. Sweets explains that there are three sides to the triangle as there are three sides to Pelant. One: the base of Pelant's rebirth and innocence. Two: his secret killer persona. Three: Pelant wants one of them to kill him, which he figured out with the help of Hodgins. Angela's face goes blank as she starts to think more about the triangle..
Brennan praises Clark and his work with his white binders. Brennan tells Cam that the murder weapon is not an axe. Brennan explains that all the photos that the team had of Pelant as a child were digital and altered, and that while on the run, Max got his hands on a real yearbook. Pelant was actually overweight; therefore, the weapon used to kill Carole Morrisey was actually lighter than an axe. Pelant's grandfather fought in World War Two and brought back a Japanese sword as a souvenir. Cam tells Brennan she will have Caroline get a warrant to search Pelant's family home. Brennan got him!
Clark removes the sword from the evidence bag and tests it out in the Bone Room. It's a match to the injuries.
Angela works at the Angelatron with the triangle code. She aligns the ends of the triangle and the code streams together.
Booth and Max watch Pelant in shackles led into the FBI. Max wishes Pelant was dead instead of going to jail.
Brennan, Cam, Clark, and Hodgins come into Angela's office. Angela shows them the image of Brennan at the crime scene. Angela runs Pelant's code and Brennan pixilates: she is no longer there. The team celebrates.
Booth and Agent Flynn enter the Interrogation Room with Pelant. Booth places the Japanese sword in front of him and smiles.
Back at Booth and Brennan's house, the gang, including Agent Flynn, celebrate their victory. Agent Flynn announces that he will be moving over to domestic terrorism and Booth can go back to the Major Crimes Unit. Caroline also has an announcement: Brennan is no longer a suspect for the murder of Ethan Sawyer and can return to the Jeffersonian. Cam is next with an announcement. The Jeffersonian needs two forensic anthropologists: one to solve crimes and one to do archaeological work. Clark is thrilled with this news, since he loves archaeological work. Booth thanks Angela for keeping his family safe while they were away from him. Everyone celebrates all the good news!
Later that night, Brennan apologizes again to Booth for all the pain he has been in during the last three months. Booth knows that Brennan did the right thing. Booth gets a call.
Booth and Brennan enter the FBI. Caroline urges the two to be civil. Caroline explains that Pelant is actually Bassam Alfayat. His fingerprints, medical records, and DNA identify him as Alfayat. In the Conference Room, Booth and Brennan can see Pelant with Egyptian government officials. They make their way out of the Conference Room. Booth asks if Agent Flynn can do anything, but he can't. Alfayat goes back to Egypt tonight. Pelant comes out of the Conference Room and hands Brennan a marigold. Brennan slaps Pelant in the face. Pelant is taken away by the FBI agents. Booth asks Brennan what a marigold means. She tells him...pain and grief.