The bodies of twin boys, kidnapped five years earlier, are discovered. The investigation lead Booth and Brennan to a notorious kidnapper known as the Grave Digger. During the investigation, Brennan and Hodgins become the Grave Digger's next victims.

Rogue sniper Jacob Broadsky returns once again, claiming another victim and making Booth determined to put him away once and for all.

The team investigates the death of a man who had offered Booth information on a possible government cover-up related to a previous case, but was killed before their meeting took place. As Booth and the Jeffersonian team dig deeper into the burgeoning conspiracy surrounding the man’s death, it’s evident Booth may be in over his head, and his future with the FBI is put in question.

The team dives back into investigating a serial killer from the past, attempting to find “The Puppeteer,” who lives with his victims’ bodies before disposing of them. Meanwhile, Brennan works through her guilt over her retirement last year, blaming herself for not stopping the serial killer earlier. However, little does she know she might be in some trouble of her own.

Brennan gets a glimpse into her own life when the body of a brilliant and career-driven surgeon is found in a rough neighborhood with multiple fractures in her skull and no indication as to how or why she was there. While the team investigates the case objectively, Brennan struggles to separate her own life from the victim’s as she perceives many parallels between them the more she learns about the victim’s past. Meanwhile, evidence found at the crime scene brings the team closer to solving the case, but it’s Brennan’s unique perspective that propels her to retrace the final events of the victim’s life. With the reassurance of a new friend and Jeffersonian security guard, Micah Leggat, Brennan makes a discovery about herself and learns a lesson about taking chances.

Brennan's new fascination with basketball and legendary coach Phil Jackson's thoughts on teamwork prompts her to gather five of her best "squinterns" to analyze remains that have never been identified.

Brennan receives some bones to identify, but is stunned when she discovers that the remains are those of her mother who disappeared when she was 15 years old. The determined date of her mother's death leaves Bones confused and angry.

When Dr. Sweets' book gets published, both Booth and Brennan read it and tell him about the first time they met: 6 years ago. The episode will give a new perspective on Booth and Brennan's relationship, and will also give viewers the chance to see Zack Addy again, and Dr Saroyan as a New York Coroner.

When a 15-year-old Jane Doe is found on the streets, it is up to Brennan, Jeffersonian Intern Arastoo Vaziri and the entire Jeffersonian team to figure out her history and if she is responsible for a recent murder

"Hacktivist" and suspected serial killer Christopher Pelant is back in court, but the team's efforts to pin another murder on him don't go as planned.

Brennan and her team are brought in to identify the body of a man found in a fallout shelter. While cutting into the bones of the man, Zach accidentally releases a deadly fungus, causing the team to be quarantined over Christmas.

The notorious serial killer, Howard Epps, sets his prison cell on fire as part of a daring prison escape. Brennan is his target and her entire team is placed in danger.

While trapped and trying to escape from a ship in the middle of the ocean, Booth is haunted by strange hallucinations.

Brennan and the team attempt to absolve Booth and get him released from prison. The remains of a man who has been dead for over sixteen years prove to be significant.

Booth and Brennan are called to the scene where a man's body was found hung like a scarecrow, gutted, and burned on the roof of a building used by the FBI to hide witnesses.

A wannabe singer Tommy Sour was found on a grassy location. The investigation leads Brennan, Booth, and Cam to the Checker Box Restaurant where Tommy used to sing. There are several suspects who took part in the open mike contest there, with talent scouts in the audience. The group comes together with a startling revelation for Brennan.

When a Jeffersonian coworker dies of heart failure, the entire team goes to the wake where, upon viewing the body, Brennan realizes the death was no accident.

Mr. White and his team of government agents put the Jeffersonian Lab on lock down and demand that Brennan and her forensics team determine a cause of death for an unidentified, but highly classified set of remains. As the team gets to work, their findings lead them to suspect they are investigating one of the most famous presidential assassinations in history. Meanwhile, Booth's boss, Andrew Hacker, helps him break into the lab and determine the motive behind the mystery investigation, and a frustrated Cam worries that Michelle may be keeping a big secret from her.

The trial of The Gravedigger hits close to home for members of the team, and everyone at the Jeffersonian must work overtime to uncover the forensic evidence to elicit a conviction.

The city anxiously anticipates the arrival of Heather Taffet, more notoriously known as "The Gravedigger," for her final appeal after being sentenced to death for a kidnap-murder and a series of similar coldblooded crimes. But when a bullet targeted at The Gravedigger is fired from a distance and hits her, the Jeffersonian team is tasked to piece together the sniper's precise location as well as identify the suspect and his motives. With the help of probing investigator Caroline Julian, Booth and Brennan put together a list of likely suspects, but the evidence and the remarkable skill needed to pull off the crime leads the team to believe that the crime was an inside, professional job, leaving Brennan's father Max and even Booth as plausible suspects. Meanwhile, Sweets attempts to put on a brave face after being caught in the firestorm just moments following a chilly encounter with The Gravedigger.

In the 6th season finale, the team investigates the disturbing, unidentifiable remains of a bowler that were found jammed in one of the bowling alley's automatic pinsetters. After hitting a dead end in the case, Booth and Brennan decide to go undercover and join a competitive bowling team in search of answers.

A cryptic message penned in human blood is discovered at a national monument. As the Jeffersonian team embarks on a scavenger hunt to solve the case, they realize their tech-savvy suspect remains one step ahead of them. Meanwhile, Booth and Brennan search for the perfect home for their new family.

Having been accused of murder, Brennan is on the run from the FBI, with help from her father Max. Booth and the Jeffersonian team are convinced evil tech genius Christopher Pelant has manipulated key evidence in the case to pinpoint Brennan as the prime suspect. Then, an anonymous tip leads the team to the remains of a high school guidance counselor that may hold the key to proving Brennan's innocence.

After Hodgins and Angela are drugged and wake up to a bloody corpse hanging in the canopy of their bed and flower petals around their son Michael's crib, they are forced to believe that Pelant is back for revenge against Hodgins. Although Hodgins wants to go after Pelant directly, Booth knows it's best to work within the system and not go against protocol. Meanwhile, as the Jeffersonian team investigates the corpse, they discover the victim was a Special Forces agent working for the world's biggest supplier of mercenaries, and Angela and Hodgins decide to start an investigation without the rest of the Jeffersonian team for the sake of their family.

The Jeffersonian team investigates the murder of Nancy Handelman, whose body was discovered at the time of Brennan and Booth's wedding rehearsal. When the case becomes more serious than the team anticipated, Cam and Angela do everything in their power to keep the details of the investigation from Brennan in order to ensure that she will stay focused on her big day. Tensions run high when unfortunate events occur to stall the wedding temporarily, and Max comes to town with a suspicious duffle bag full of money.