A cabin burns down in the woods revealing two bodies, one of a modern-day witch and one from the days of the Salem Witch Trials leading Booth and Brennan into the world of Wicca to find a killer. Meanwhile, when Hodgins' reckless driving gets him and Angela arrested and thrown in jail, Sweets and intern Clark Edison step into unfamiliar territory to help out the team

A psychic joins the investigation of a death of a little boy whose soul is believed to be still alive, prompting the team members to reflect on their beliefs of life after death.

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.

A competitive eating champion's body is found shortly before the next major competition. Following a disagreement over the baby, Booth and Brennan attempt a little role-playing. Back at the lab, Brennan's new assistant seems a mismatch, despite his genius.

With the help of Special Agent Genny Shaw, the Jeffersonian team identifies the remains of a discount shopper and “extreme couponer” who was dragged along the road by an 18-wheeler. Meanwhile, Brennan is adjusting to her first day back at work after giving birth, and Cam disapproves of her daughter’s romance with intern Finn Abernathy.

When an actor known for playing a popular character on a kids' TV show is murdered, unexpected suspects are discovered; Brennan and Booth plan a party for Christine's birthday; Clark asks for opinions on his novel.

When the body of an ex-con is found in pieces, the Jeffersonian team investigates a local bakery known for employing former felons.

When the remains of a competitive gamer are discovered in a grease truck, Brennan and Booth are called to investigate the case. The victim, Steve Rifton, is the only active player known in the gaming community to have received a perfect score on a famous video game. Steve turned his success into a lucrative partnership with a gaming referee and charged fans to play on the very machine that gave him the perfect score. But between sour business deals and bitter competitors, the team at the Jeffersonian must work to narrow down the many suspects with motive for ending Rifton’s reign as gaming king. Meanwhile, Hodgins, Sweets and Jeffersonian intern Colin Fischer take turns camping out for tickets to a movie premiere.

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.

The team discovers the remains of a so-called "storm chaser" who seems to have died while following a tornado. But footage recorded during the storm ultimately leads them to believe he was murdered. Meanwhile, Booth becomes increasingly overprotective of Brennan both at home and in the field, and sleep-deprived Angela and Hodgins come to terms with having Angela's father and rock musician babysit their infant son.

When a corpse is found at a landfill, dyed in a blue substance, intern Arastoo Vaziri discovers a method that helps eliminate postmortem damages to the corpse, which leads the team back to a hair salon where the victim worked. Meanwhile Bones is feeling uncomfortable in her post-baby body, so Booth decides to do something special to boost her self-confidence.

The Jeffersonian team investigates the death of a professional ballroom dancer who was murdered three days before her audition on a popular dancing competition show. In order to solve the case, Brennan and Booth go undercover as dance competitors to see if they can find potential suspects.

The Jeffersonian team investigates the murder of a TV producer. Meanwhile, Brennan has trouble accepting the fact that Christine might be an "average" child, when her daughter gets accused of biting another classmate. Then, Hodgins uses all of his tools at the Jeffersonian to chemically recreate Finn's special hot sauce.

The Jeffersonian team investigates the murder of Jason Siedel, an accountant for the state department, whose remains were found in a hotel air conditioning unit. When Booth finds his old army buddy and CIA agent, Danny Beck, clearing away evidence at the victim's condo, he begins to realize that Siedel's murder could yield more suspects than the team had anticipated. Booth also seeks out Aldo Clemens, his friend and an ex-priest from their military days together, to get advice on his relationship with Brennan, now that Pelant has put a wedge between them. Meanwhile, Brennan must decide whether to have faith in Booth or to end her relationship with him.

The team investigates the death of a woman whose body was cryogenically frozen before being dumped in a swamp; Cam is nervous to meet Arastoo's parents; Booth is up for a promotion.

A body discovered in a hot spring turns out to be that of Tripp Goddard, a sexy motorcycle racer who had disappeared two weeks earlier. Sweets talks Booth and Bones into going out with him and his girlfriend.

When a human skeleton is discovered in the trenches of an old Civil War battleground, Brennan and Booth are called to the case. Despite the historical location, Brennan quickly identifies the bones as belonging to Dan Pinard, a present-day local dentist. While Booth investigates suspects, including the victim’s former boyfriend, Hodgins and lab intern Vincent Nigel-Murray work doggedly to clean the bones of a stubborn clay residue which is preventing the team from determining a cause of death. Meanwhile, Booth’s brother, Jared, returns from his travels with some suprising news.

Booth and Brennan investigate a death at a rock-n-roll fantasy camp where the murder weapon is a Gibson ‘57 Les Paul “Black Beauty.”

The team identifies the remains of a successful ad man found in the grounds of a newly built community center playground. Upon inspecting the victim’s home and interrogating his former partner and employer, Booth and Brennan discover that the victim burned bridges by adopting an aggressive attitude toward honesty and was a member of a radical honesty support group. Meanwhile, each of the team members attempts to adopt a more honest way of communicating that doesn’t always lend itself to good relationships, and Angela urges Hodgins to confront the realities of their pregnancy

The Jeffersonian team investigates the murder of Jack Spindler, a successful employee at a brokerage firm by day, but a stripper by night. When the team learns how Spindler's moonlighting affected his personal life, they start to question the people closest to him, including his stripper friend, Storm. Meanwhile, Booth's mother shows up after a 24-year absence in his life and makes a special request of him.

The team suspects that a man who made his money donating sperm was killed by a recipient who learned his records were inaccurate; Brennan enters a feud with a fellow author (Nora Dunn).

The case of a maid's death turns out to be a bigger case than originally thought. Tensions are rising between Cam and Brennan.

The team investigates the high-stakes murder of a political journalist who was found dead after recently publishing an article exposing corruption in the NSA. Due to the nature of the investigation, Hodgins’ paranoia takes over as the team realizes their every move is being watched. Meanwhile, Brennan secretly tries to plan a surprise for Booth and the whole team celebrates Thanksgiving together.

The corpse of a truck company employee is found in the middle of the woods. After the victim’s son is questioned, Booth and Brennan visit his karate class in search of a motive. Back at the lab, Hodgins is going overboard purchasing lab equipment. Then, Booth’s son Parker returns from England and Brennan is apprehensive about how he’ll react to his new baby sister.

When the remains of a repo man are found in a septic tank, the team learns he had a troubled past; a forensic anthropologist (Ignacio Serricchio) who has defected from Cuba needs an internship.