A group of teenagers are driving when a skull smashes through the windshield. Brennan tests a young forensic anthropologist as a replacement for Zack, while she and Cam inspect the skull. The find human teeth marks on the skull, suggesting that cannibalism may have been involved. Once the victim is identified, Booth and Brennan head out into the field and clues lead them to a cannibalistic society. Meanwhile, Cam suggests hiring a private investigator so Angela can track down her ex-husband, but that proves to be easier said than done.

Brennan and Booth are put on the case when a soccer mom is blown up in her minivan. The team discovers that the mother had once been a member of the National Liberation Army during the 1970s and the FBI had been trying to track her down since. But when the team learns that June may have been on her way to turn herself in, the motives for her murder become more complex. Meanwhile, Brennan visits her father in prison and Booth gives her advice on the situation.

An 11-year-old camper comes across a decomposed body of a man with his feet removed and arms bound. The team heads to the woods to investiage and clues lead them to a Virginia lodge used for an S&M; retreat where women act as jockeys and men act as their horses. Several people become suspects, including the victim's wife. However, Zack and Hodgins find evidence that makes finding the killer more difficult than expected. Meanwhile, Angela agrees to use hypnosis to help her remember the name of her husband so she can get a divorce and marry Hodgins, but she has difficulty falling into a trance.

Booth and Brennan are called when teenagers find a decomposed body near the grounds of the VA hospital. They identify the man as Franklin Curtis, a man who founded a chain of organic supermarkets. Investigation of the body by the team concludes that the man had been cooked or incinerated after his death. Booth's main suspect is a rival farmer, but when the flesh of another body is found on Curtis's body, the team is lead to believe it was a double homicide. Meanwhile, Booth and Brennan are assigned to undergo counseling with psychiatrist Dr. Lance Sweets.

A Halloween maze-goer finds mummified remains of a teenage girl within a pumpkin patch maze. Booth and Brennan are perplexed by the fact that the girl had been dead for at least a year, and Hodgins later finds that her body is covered in spider bits. When a second mummified victim is found in a Halloween park funhouse, the team must question park employees before another teenager falls victim. Meanwhile, the team dresses up for the annual Jeffersonian Halloween Ball.

The charred remains of a young Jeffersonian intern, the daughter of a highly respected former Jeffersonian scientist, are found in the building's incinerator. With the case hitting so close to home, the team has no choice but to suspect their own colleagues and question everyone from the upper echelons of the Jeffersonian scientists to the victim's fellow interns. When they learn that the intern had been working on artifact authentication for the Widow's Son serial killer case, they begin to wonder if her involvement could have put her life in danger. But when they discover a romantic link between the intern and a Jeffersonian employee, the motives behind her murder become even more complicated. Meanwhile, Booth agrees to pose as Cam's boyfriend and accompanies her on a family get-together, eliciting more attention than he bargained for from Cam's sister

A group of high school alumni gather to unearth a time capsule buried 20 years prior, only to find the body of one of their former teenage classmates inside. The victim, identified as a shy, ostracized classmate, leads Booth and Brennan searching through the class of 1987's high school secrets as they rehash some high school memories of their own. With psychological profiling advice from their young therapist, Dr. Sweets, the team's investigation has them exploring timelessly familiar high school stereotypes the geeks, the outcasts, the jocks and the cheerleaders in an effort to discover the murderer

After construction workers find the body of an archbishop whose kneecaps were surgically removed, the team is back on the case of the Widow's Son serial killer. When Angela discovers what appears to be a victim tree in the evidence vault, the team realizes the killer employs a systematic pattern in selecting victims. With a musician and an archbishop the first to go, the team tries to predict who might be next and how they can stop the killer before he strikes again. Brennan and Booth continue to see Dr. Lance Sweets, who has some helpful psychological insights into the Widow's Son's motives. Meanwhile, Brennan's brother, Russ, comes out of hiding when he finds out that his girlfriend's daughter is extremely sick, but his appearance causes Booth to intervene with Brennan's family once again.

Booth and Brennan are called to the scene when a body is found in a sewer. The team is shocked when all clues point to the victim being Santa himself and are even more miffed when the victim's legal name turns out to be Kris Kringle. While following the clues in order to find the man's killer, more evidence comes about that makes the team suspect that he's the real deal.

A young couple goes skinny-dipping in a spring, but their moment of fun is ruined when they uncover a skeleton in the mud. Brennan and Booth are called to investigate and find that the skeleton is that of Tripp Goddard, a motorcycle racer who recently won the Super Grand Prix. The first suspect is Danny Fitz, the race's second-place finisher. However, though Booth and Brennan think they have the case wrapped up, another crash claims another victim in suspicious circumstances. Meanwhile, Dr. Sweets has Brennan and Booth go with him on a double-date in order to get them into another social setting together where they have to interact away from a case.

Brennan and Booth are called to a college campus when remains are found under the bleachers of a basketball court. Though the body was badly crushed, a gold necklace with the number 11 on it helps to identify the victimas the star point guard of the school's nationally ranked basketball team. When the team reconstructs RJ's skull, they find that he was dead before the bleachers crushed his body. Taking this into account, Brennan and Booth uncover several motives and suspects for RJ's murder.

Booth and Brennan are called to investigate when a body is found burned beyond recognition in car that was run off of the road. As they investigate, the team finds the victim's baby in a tree avbove the scene of the accident. Brennan is designated as the infant's caretaker until family can be reached, but her mothering skills are questioned when the baby swallows a piece of evidence. Once the victim is identified, Booth and Brennan head out to a poor Virigina town to look into who may have wanted the woman dead.

Max goes on trial for the alleged murder of FBI Deputy Director Robert Kirby, and the Jeffersonian team members, minus Brennan, are called as expert witnesses for the prosecution, keenly aware that their testimony could put Max on Death Row. Brennan, serving as a forensics advisor for the defense, must rely not only on her expertise as an anthropologist but also on her dedication to her family to find a way to exonerate her father.

Brennan and Booth investigate the murder of singer Tommy Sour, including his many fans and enemies within the music scene. But their search leads to a woman obsessed with the singing star, who now has redirected her admiration towards Booth, now that Tommy is dead. The Jeffersonian team may be changed forever when a shocking event is revealed during the investigation.

When a human jawbone shows up at the Jeffersonian, Brennan and the team quickly realize that the Gormogon serial killer has struck again. In a shocking turn of events, an explosion in the lab sends Zack to the hospital; Gormogon's silver skeleton goes missing from the basement vault; and every Jeffersonian employee becomes a suspect, with the very real possibility that one of their very own may be working with the twisted and elusive serial killer.