When a man is killed driving an SUV registered to a Middle Eastern man, Dr. Brennan and her team find themselves tracking a terrorist.

When Brennan decides to give online dating a try, she ends up the target of a shooting at the local restaurant where she's meeting her date. The resulting investigation reveals that the shooter could be connected to either of the two cases she's currently working on.

Brennan and Booth investigate an apparent suicide in Arlington National Cemetery, but soon discover it is a murder linked to a military cover-up.

When the remains of a young pregnant woman and fetus are found in the Delaware Bay and identified as a newlywed who disappeared a year earlier, the investigation is aimed toward her husband, but takes a surprising turn. Booth is upset that his ex-girlfriend is letting their son spend time with her new boyfriend.

The team investigate a glowing body. Hodgins proposes to Angela -- several times.

The Gormogon serial killer is back again, and the silver skeleton from the basement vault has gone missing. All the Jeffersonian employees become suspects, with the scary possibility that one of their own is working with Gormogon.

With the case of the murdered heiress solved, Booth and Brennan prepare to head back home, but are shocked to learn of another murder - and this time it's someone they know. Meanwhile, with Birimbau unexpectedly coming back into Angela's life, things get complicated between her and Hodgins.

The team is on the case when human remains are found inside a barrel of wine during a wine tasting. When the victim turns out to be a wine critic whose scathing reviews were capable of sending a vineyard to its ruin, everyone from the winery's owner to the victim's own wife becomes a suspect.

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 team works to uncover clues buried under a life’s worth of possessions saved by a hoarder in order to solve the mystery of his death. Meanwhile, Angela’s father has a specific purpose for his most recent visit, and Brennan and Booth are confronted with unique opportunities.

When the remains of a couple are discovered in a cave at National Park, the team must piece together the identity of the man and the woman as well as solve the crime. After interrogating two viable suspects, the team identifies the woman as a marketing executive who also served as her partner’s AA sponsor, providing clues that lead them to expose the truth. Meanwhile, Booth’s girlfriend and Afghanistan war correspondent, Hannah Burley, makes a surprise visit. After meeting Burley and sensing the couple’s genuine happiness, Brennan re-evaluates her own relationship with Booth, and he tries to teach her that love is not always logical.

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

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.

The body of a woman found buried under a paintball field yields more questions than answers as the investigation into her death reveals even she didn't know who she was. On the domestic side, Booth and Brennan adjust to sharing space with each other… and her growing stomach.

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.

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.

When evil tech genius Christopher Pelant returns to toy with the Jeffersonian team in their newest investigation, they discover that the string of murders that have been occurring are tied to FBI agents close to Booth. Meanwhile, as the investigation unfolds, Sweets realizes that the evidence seems all too familiar to him and Brennan starts evaluating her relationship with Booth when signs begin to point to him as a potential target of Pelant's.

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.