Three teens are in a car on the highway. As they go under a bridge something is dropped from it, bounces off the top of a dump truck in front of them, and smashes into the teens' car. It's a human skull.
Cam and Brennan are questioning Clark Edison, a possible replacement for Zack. Cam seems pleased, but Brennan is obviously upset about the whole thing. Booth arrives and asks if "Bones" is interviewing Edison. Cam introduces both men, and Edison mentions that "Bones" was his nickname in college. Brennan is not amused and Booth asks her if she's got a minute. Edison asks if they need him at the crime scene and Brennan tells him they'll let him know. Cam tells Edison that he's doing fine, but he's certain he's not impressing Dr. Brennan.
At the crime scene, Booth and Brennan argue as they approach the car. Booth accuses her of not wanting to come out to the field anymore and Brennan defends herself saying that with Zack gone, she has a lot of work at the lab. Booth tells her that she's not even bothering to correct his scientific mistakes and Brennan just asks him what she's doing there. Booth points to the inside of the car, where the skull is still embedded in the windshield.
Booth comments that it's been over 3 months since Zack got shipped off to Iraq and wonders how hard it could be to replace him. Brennan ignores him and starts her initial diagnosis on the skull. Booth presses on, mentioning that they're not working to their full "symbiotic potential" as Brennan continues to ignore him. Booth tries to get her attention by tapping on the windshield with a pen, saying that maybe she doesn't want to work with him anymore. She brushes it off by being literal and keeping her focus on the case.
Both brings over a witness, who might not be too credible, as the car reeks of weed, but he claims he's sober. Brennan asks the boy a couple of questions regarding where the skull came from, but both of them are dubious. Brennan begins weaving different possible scenarios until Booth points to an overpass bridge. Brennan wonders who'd drop a skull from up there in the first place.
Angela and Hodgins meet with Doug Doyley, the private investigator who's looking for Angela's "husband". The marriage certificate she has is no use, as the man signed it with an X. The detective asks Angela if she married a guy without knowing his name and Angela tells him that it was Fiji and she was on vacation (so yes). He also asks if the marriage was consummated, which upsets Hodgins, but Angela says it was. Hodgins mentions they want to have the marriage annulled, and that they need consent from both parties to do that. Doyley asks for a description, photographs, and other witnesses, but all Angela can come up with is that the guy was tall, muscular, and black, and that his name MIGHT have a B in it...or maybe a K...and she offers to make a sketch.
Back at the lab, Brennan tells Cam of her finding on the skull; she's particularly interested in some sort of scrapings, whereas Cam is more interested in knowing if she has made her mind up yet about hiring Clark Edison. Brennan tells her she hasn't decided yet. Cam tells her it's okay to take her time, but that Brennan has already turned down 17 applicants, and their field is not that common and they're running out of options. Brennan continues working on her skull findings, telling Cam she'll cover the lab work until they find the right person.
Brennan calls up Booth, who seems delighted, as she hasn't called him in weeks. She tells him of her finding as he walks towards his SUV eating a sandwich. He gets some of her scientific jargon right ("I know what scoring means") but completely messes up on the important part. Brennan is reaching for a way to explain it to Booth and Cam finally breaks in to tell him that the teeth that did the damage were human. Brennan sums it up by saying the victim's face was chewed up by a cannibal. Booth stops chewing the sandwich he was eating and throws it away.
Booth and Caroline are trying to figure out where the dump truck came from, hoping to find the remaining body there. Back at the lab, Brennan and Edison have discovered a distinctive bone characteristic in the skull that will help them identify the body. Angela comes in to tell them that Booth is bringing in huge amounts of bone chips from the landfill and threatening to bring back more. Brennan walks out and Angela follows her, accusing her of not wanting to hire Edison. Brennan sticks to her line of not having made up her mind yet. Angela tells her that she's just stalling to not go into the field with Booth, and she tells Brennan it's because she's running away from the repercussions of having been left with him in front of an altar, and all its symbolism. Brennan denies understanding what Angela is talking about. Angela tells them they'll talk about it later, when Brennan is ready to face the truth.
Booth arrives at the lab as Brennan and Edison are going over the bone chips, and he asks Brennan to join him in the field. She excuses herself once more, claiming that there's a lot of work to do, and Edison offers to do it by himself. Brennan tells him it's too much work for one person and Edison is about to disagree when he catches the look on her face. Booth catches it, too, and asks the young man if it's true. Edison bows out claiming they're putting him in a very awkward position. Booth leaves, telling Edison that Zack would have told him.
Later that day, Booth and Cam are having drinks and he's complaining about the whole situation. Cam asks him if he's feeling guilty about something and he tells her he's still feeling bad for having arrested Brennan' father. He justifies his actions telling Cam he asked Brennan if she was okay with it, but Cam tells him no one is that rational, and something like that is sure to cause some stress on any relationship. Booth complains Cam is not helping him any, and she tells him next time he wants sympathy, not to ask a close friend.
The skull is identified as Gavin Nichols, violin virtuoso, missing for a month. Booth and Brennan start exchanging theories and Booth mentions once more how symbiotic they can be when they work together. Brennan ignores him again and he asks her to join him for the interrogation. She tells him she can't as she found some grit on the skull. Booth gets upset, and tells her that's Hodgins' job. Brennan tells booth she needs to supervise it. Cam tells Booth to take Angela instead.
Booth interrogates Gavin's girlfriend while Angela looks at the pictures the girl brought with her. Booth cannot find anything suspicious and is about to let her go when Angela points out to a specific picture. Angela guesses the girlfriend looked sad in it because she knew Gavin was going to die, but Booth figures out it's because he was having an affair on the side. His hunch pays off: Gavin was having an affair with the wife of the Deputy Director of the Secret Service.
Hodgins identifies the grit and tells Brennan it's very rare and can only be found in the D.C. area in a couple of very specific buildings. He also tells Brennan to forget about replacing Zack and just try to find someone to help them out.
When interrogated, Mrs. Sumner admits to having an affair with Gavin and that her husband knew about it. They give Booth and Caroline video proof, and after viewing it, Booth agrees they didn't kill the boy. He just charges the husband with voyeurism.
Booth comes looking for Brennan, saying they found the place where the murder probably took place, and he asks her again, to go with him. She claims to have work to do, but this time Cam nicely orders her to go, since it could very well be the place where ritualistic killings have taken place. They go to an abandoned bank that has an underground sealed vault.
They get the door open and find an almost museum-like collection inside. Booth finds a ticking device on the inside of the door and throws Brennan to the floor, covering her with his body. Brennan tells him it's a communication device and not a bomb. They continue searching the vault and find a silver skeleton with several real bones replacing different parts.
Upon further investigation, they find more gnawed-on bones, Gavin's violin, and an altar made with the same material they found in the skull. Angela tells them the whole setting is medieval, probably Spanish – Calabrian. Hodgins goes off telling them about the Order of Alcantara, part of the Illuminati sect, but they cut him off. Caroline wonders if this is a serial killer they're looking for, and agrees to have the whole thing shipped to the Jeffersonian.
Doyley tells Angela and Hodgins that the "priest" who married Angela died in a tsunami and that the island is now deserted. Angela tells him she was drunk and can't remember anything, not even enough for a sketch. Doyley leaves, hoping to find an Australian ship that was docked there that day.
Booth arrives at the lab to find everyone working on the findings inside the vault, and tells Brennan that now everyone is helping her. The rest of the squints tell him it'll take months to sort through all the stuff, and Booth accuses them of enabling someone with a mental condition. Brennan stops talking and points behind him: Zack just walked in. The whole squad runs down to greet him and he tells them he wants to get back to work right away. Booth tells Edison it was nice meeting him as he figures out he's not getting the job.
Zack analyzes the skull and finds a strange scraping which leads Brennan to believe it was done by a diamond inset on a tooth. She tells Booth of the finding and asks to join him for interrogation. Booth is surprised, but happy about her change of attitude.
They interrogate Jason, a young man who was doing community service by keeping the old bank clean. They tell him that they know he's guilty because of his diamond tooth. Brennan asks him to bite on a piece of wax to get an imprint, then Jason starts telling them about the taste of human flesh.
Zack can't go to sleep due to the time zone difference and has been working on the bones they found. He's found out they belong to six different people. Cam asks him why they sent him back from Iraq, and Zack tells her he never managed to fit in.
Doyle shows Angela and Hodgins a picture of some of the Australian sailors and she recognizes one of them: a fairly huge guy. He also found out his name and his nationality and a possible location. Doyle tells them that if they wait 3 years they can declare him dead, but neither Angela nor Hodgins wants to wait, so they ask Doyle to keep searching.
Booth and Brennan go back to the lab, responding to Zack's urgent call, and find him resting on top of an autopsy table. Brennan looks at his findings and tells Booth they have a second cannibal...probably the one who got Jason involved in the first place. They go to jail wanting to talk to Jason. While they wait to see him, they argue as to why Brennan is mad at Booth. It all boils down to Booth letting Zack go to Iraq. Booth tells Brennan that the young genius needed to leave the nest and that she did the same type thing once.
The jail deputy leads them to Jason's cell, where they find him stabbed and placed in the same position as the silver skeleton. They ask Hodgins for his input and he tells them that the position is known as "pharmacus" or scapegoat, and that the Freemasons referred to it as "The Widow's Son". Cam's points out that Gavin's father died when he was 12 years old.
The whole team is left with more questions than answers as they reach the conclusion that there is a killer loose out there and, as Hodgins points out, they "might end getting themselves killed".
Sitting on a bench outside, Booth tries to get Brennan to take the hot coffee he brought her, while she rambles on about the case. He stops her from drinking the hot coffee by putting his hand over the cup right as she is about to drink, and she says thanks you. Booth wants to know if they are solid, and Brennan thinks he is just talking about her and him, but he says that it is the whole team. They are the center of the team, and he wants to know if they will hold. She says, yeah, they will hold, and puts her hand out to shake his hand. He laughs, and tells her he thought she was going to kiss his hand again, and she says she did not kiss his hand. Booth says it felt like she kissed it. The scene fades out with them drinking their coffee, with their relationship back to normal.