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As Special Agent Booth drives Dr. Brennan to the crime scene, they discuss Brennan's vacation and her decision to keep looking for her father, despite his warning (in "The Woman in Limbo"). They arrive at the crime scene, where a train has derailed after crashing into a parked car on the tracks.
On December 23, Booth brings in the skeletal remains of a man found dead in a bomb shelter discovered recently. Everyone is in Christmas-Eve mode with a company party going on upstairs. Bones and the rest of the team start investigating the dead man's story when Zack triggers the bio-hazard alarm while cutting through the skeleton.
Booth and Brennan visit the home of the man Booth suspects of the murder of the college girl, Kevin Hollings. They find a knife with no nick on the blade and a collection of thousands of keys. While Hollings refuses to talk, Brennan realizes that the keys could be what was used to gouge out the eyes of the victim and orders a photo of each key ...
Brennan surprises Booth under a gazebo and proposes. Sweets warns Booth that he and Brennan getting engaged with Pelant active could cause him to escalate. Angela determines that Pelant has access to every security camera with an internet connection. Later, Booth and Brennan are at a park with Christine.
Initially Bones' father Max (Ryan O'Neal) is listed as a suspect due to his criminal tendencies, but when the team discovers that it was a professional hit, Booth, a former Army sniper, is forced to question an old Army colleague. Sweets deals with the aftermath of the shooting, due in part to his close proximity to her when she was killed, but ...
Booth returns to the FBI after being certified by Dr. Sweets and wonders if his feelings for Brennan are real or if they are just the effects from his brain surgery. Angela's psychic Avalon (Cyndi Lauper) leads Booth and Brennan to a crime regarding bodies being buried under a fountain in Washington, one of which is Avalon's younger sister.
Bones has nightmares about what Pelant told her about the female serial killer, "The Ghost Killer". Remains of a girl named Lana Brewster are left at Booth and Brennan's doorstep with a note saying to solve her murder. The dreams start to interfere with her job and Cam gives the remains to Clark.
She wants Booth to let Margaret go so she, Shawn and David can continue to be a family but Booth remains resistant. As Angela works on isolating the image of Charlie's abductor in the surveillance footage, she learns from Zack that Hodgins is extremely wealthy; his family runs the organization that is the single biggest donor to the Jeffersonian.