Three Sk8r kids are driving around, getting stoned when a dump truck ahead of them suddenly sends a small, round object smashing through their windshield and causing a chain reaction collision.
Back at the Lab, Brennan and Cam are quizzing Clark Edison, a candidate for Zack's job. The kid is good but Brennan still has reservations. Booth arrives to pull her out to the crime scene. She doesn't really want to go, and this bothers Booth.
Near the Sk8r kids' car is a highway littered with broken, smoking cars. Booth and Brennan make their way through the commotion. Bones is complaining about Booth pulling her out of the Lab, when she notices a human skull embedded in the teens' windshield.
They talk to the Sk8r driver, and that's when Booth and Brennan realize the skull was dropped, not from the dump truck, but from a nearby overpass.
Meanwhile, Angela and Hodgins meet with Doug Doyley, a private investigator. They are trying to have Angela's marriage annulled. Hodgins has hired Doyley to hunt down Angela's first husband. Unfortunately, Angela can't seem to remember his name. All she knows is he's tall, muscular, and black. She'll have to draw the P.I. a sketch.
At the Lab, Brennan checks out the skull. Cam enters and voices her frustration at Brennan's inability to choose a new assistant. Brennan gets on the phone with Booth.
She has news for him; the skull has scoring on it - very strange scoring. It looks like it's been gnawed on...by a human.
Booth is in the conference room with Agent Charlie and federal prosecutor Caroline Julian. Booth has evidence that suggests the rest of the body might be in a landfill. That's where the dump truck was headed. Booth wants a warrant to check it out.
In the Bone Room, Brennan, Cam, and Clark, who is still eagerly trying to impress Brennan, study an x-ray of the skull. They've discovered an osteoma: an identifying anomaly that serves as a bone version of a fingerprint. The Squints will look to match it with the records of any local ear, nose, and throat surgeon. Brennan learns bones have been found in the landfill and she hurries off to look at them.
Angela pulls Brennan aside. Angela is convinced Brennan won't replace Zack even though Clark is a great choice because Brennan needs an excuse to avoid going into the field with Booth. Brennan has no idea what she's talking about. Angela tells her it freaked her out to stand next to Booth at the alter during Angela's aborted wedding ceremony. Brennan denies this.
In the Lab, Clark rummages through the pile of landfill bones with Brennan's help. Booth tries to get her to come into the field with him, but even after Angela's scolding, Brennan won't go with him.
Later at the bar, Booth and Cam sit and drink. Booth wants Cam to overrule Brennan and hire Clark. He thinks Bones is avoiding him because he arrested her father. A call comes in: the victim has been identified.
The osteoma paid off for Brennan. Health records prove the skull is that of Gavin Nichols, a violin prodigy, who went missing a month ago. Gavin's violin was worth three million dollars. Booth wants Brennan with him when he questions the victim's girlfriend. But again, Brennan has an excuse. Cam instructs Booth to take Angela instead.
Booth interrogates Amelia Trattner, Gavin's older, thirty-something girlfriend. As Booth questions Amelia, Angela, from behind a two-way mirror, listens through an earpiece. They learn that not only was Gavin's violin worth big bucks, his little finger was insured for ten million. Angela makes some helpful suggestions and Booth gets her to admit that Gavin had a "thing" for older women - he was seeing someone besides her.
Enter Rona Sumner, the middle-aged wife of the Deputy Director of the Secret Service, Leo Sumner. Booth has a lot of questions.
In the Lab, Hodgins has found rare granite particles on the skull. He wants Brennan to pass it onto Booth. She's too busy she says because she hasn't found a replacement for Zack. Hodgins has some advice for Brennan; she needs to stop thinking about replacing Zack and start thinking about just getting somebody to help out. It's clear Hodgins misses his friend.
Booth and Caroline talk to Rona Sumner and Leo Sumner in the interrogation room. In front of her husband, Rona is surprisingly open about her sexual relationship with Gavin. Turns out the couple are swingers as Rona casually admits she was "with" Gavin the night of his disappearance. She insists she didn't kill him. Both Booth and Caroline have a hard time believing her husband knew about and accepted her affairs. They think the Sumners cooked up this story after the murder. But Rona hands Booth a DVD.
Caroline and Booth play the DVD. They're surprised to see Gavin and Rona having sex. It's clear somebody is secretly filming them. That somebody appears on the video: it's Leo. It's obvious the Sumners didn't murder Gavin. But that doesn't mean Leo, who after all is the Deputy Director of the FBI, isn't going to suffer consequences.
Booth enters the Lab with news: he just arrested Leo Sumner for voyeurism. Cam is quick to comment on that move coming back to haunt him. Booth turns his attention to the case: he's learned that the rare granite found on the skull is from an old Victorian bank that has been closed for years. Cam dubs it, a "serial killer heaven." Booth is ready to go check it out and wants Brennan to join him. Cam is finally able to convince her.
Booth and Brennan arrive at the Victorian bank accompanied by a DC beat cop. The cop leads Booth and Brennan to a locked vault. They watch as an FBI safe cracker breaks it open. Booth and Brennan enter the vault to find a steel labyrinth full of Masonic artifacts. They find an ancient Greek phrase on the back of the door, and Gavin Nichols' missing three million dollar violin. But the topper is a silver skeleton made partially of human bones. In fact, it appears that Gavin's valuable little pinkie is now part of the skeleton.
In the deserted bank, Booth, Brennan, Hodgins, Cam, and Angela have gathered with Caroline. It seems the human bones in the silver skeleton also have gnaw marks. Hodgins has his theories on the place and offers the possibility that it's a cannibalistic secret society. Brennan wants the contents of the room moved over to the Jeffersonian for further examination. She thinks more than one body was used to make the skeleton. And that means there is more than one victim.
P.I. Doyley has new information on Angela's husband. He part of a steamer crew that was docked on the island during the time of the marriage. Hodgins insists Doyley track down that steamer.
At the Lab, the Squints and Clark are gathered around the human bones from the vault. Booth shows up to finally resolve things with Brennan just as Zack surprises them. He's back from Iraq. Everybody is happy to see him. As a jobless Clark walks off, Zack is ready to get back to work.
Zack looks at the bones and suggests Gavin's skull was cooked before being eaten. He also thinks another set of teeth may have made the marks on the skull. They don't match the ones found at the landfill.
Over in Booth's office the results are in, and Zack is right. The gnaw marks on Gavin's skull were caused by a human tooth that has a diamond inset. The hunt is on for anyone who might have had access to the closed bank, including a cleaning crew, with a diamond tooth. Brennan, to Booth's surprise, wants to help him.
Booth and Brennan have found a suspect. They interrogate Jason Harkness, a creepy teen. Jason's been doing his community service at the old bank. He belligerently cops to eating humans.
In the Lab, Zack has discovered that the ten human bones on the silver skeleton belong to six different victims. None of the Squints have any idea what Jason Harkness was trying to create.
Angela and Hodgins are at the diner with Doyley, who's brought a few pictures with him. Doyley thinks Angela's husband is a sailor, nicknamed Birimbau, who might be Brazilian. Hodgins and Angela want the search to continue.
Booth and Brennan are called into the Lab where Zack has big news for them. Turns out the gnaw marks were made by two different cannibals. Jason's incisor marks are only a match on the newer bones. It appears Jason is the protege of an older cannibal.
Booth and Brennan rush over to the jail to speak with Jason. While waiting for the guards, they discuss Booth's theory on why Zack left. Booth states that Zack went to Iraq because he needed to "leave the nest" and experience life, much as Brennan once needed to do. A guard arrives and leads them over to Harkness' cell but Harkness is dead, hanging naked with a dagger through his heart. His body dangles from the bars, positioned like the silver skeleton.
Because of his body position, the group is suddenly curious about Hodgins' theories. The skeleton was deliberately posed in the "Widow's Son" position, a stance that holds deep roots in many secret societies, including the Freemasons. For the Free Masons, it represents sacrifice. And since Harkness was found with a dagger through his heart, it's now a question of who - and how many - have done the human sacrificing. There's still a lot of work to be done to find that answer.
Early the next morning Brennan and Booth finally have a chance to talk. They work things out with each other, and it looks like they're back to being normal partners.