Framed for a crime she didn't commit in the Season 7 finale, Dr. Brennan went on the run at the end of last season's "Bones," abandoning her husband and taking their baby with her. Dr. Brennan's dad, Max, is helping the two keep a low profile, while Brennan is rocking a blond dye job to help make her unrecognizable. At the start of the episode, she's been running for three months.
Angela is working tirelessly to prove that the security footage, which featured Brennan, had been doctored, while Booth keeps on hunting computer whiz Christopher Pelant. Both Angela and Booth are getting resistance from the rest of their respective staff members. The FBI can't follow any more leads on Pelant because they feel there's nothing there, while Angela is told she needs to turn her focus to other cases.
Dr. Brennan, ever the professional, felt obligated to call in a homicide to her team, which could result in her capture. Angela tells the team at the Jeffersonian that solving this murder could implicate Pelant and help bring Brennan home. It turns out that the victim is Pelant's former guidance counselor.
Booth tracks Bones down, and the two share a passionate kiss on the floor. Back at the lab, the team learns that a red agate was used as the murder weapon, and Angela discovers that electronic signatures used to discredit Brennan and Ms. Julian were forged. The team also discovers that Pelant likely forged the recommendation he got from his guidance counselor.
Angela asks Hodgins to bring flowers to a certain location as a message for Dr. Brennan. There, Hodgins finds Pelant waiting for him and throttles Pelant with his bare hands. After that incident, Angela and the team are questioned by FBI Agent Flynn, though Hodgins only reveals his violent interaction with Pelant to Sweets later on.
Hodgins and Angela help Booth and Brennan sneak into the lab after everyone goes home. Dr. Brennan finds that the victim died after being hung upside down, gutted, and bled: The guidance counselor was snared and hit her head on red agate when she flew into the air.
Booth and Flynn are able to arrest Pelant for violating his parole, giving the Jeffersonian team time to build their case. But just when it seems like their case is coming together, Pelant finds a way to escape. The Egyptian government extracts Pelant, claiming he is an Egyptian national. The marigold Pelant gives Bones at the end stands for pain and grief. But Agent Flynn picks up the discarded marigold after Bones and Booth leave. Was the message meant for Bones or for Agent Flynn?
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