The Jeffersonian team investigates the remains of two bodies that were found at the same burial plot: one of a female cancer patient; the other, the cancer patient’s “doula,” who was guiding her through her grieving process with the illness. Meanwhile, with a spotlight on the case, Brennan and Booth start discussing their individual choices for after-death arrangements. Also, Daisy Wick returns for her first case after her break-up with Sweets.
40 minS1:E1
Pilot
Pilot episode. After returning to Washington, D.C., renowned forensic anthropologist Dr. Temperance Brennan is called in by FBI Special Agent Seeley Booth to aid an FBI investigation involving a set of bones found hidden in a lake.
When the decaying corpse of the Venezuelan Ambassador's son is found hanging from a tree on the campus of an exclusive private school, a simple suicide case quickly turns into a web of lies, sex and scandal involving the school's staff and students.
When Brennan and Angela get caught in a fight in a dance club, Brennan kicks someone into a wall, which causes the wall to break open and reveal a mummified corpse and a meth stash.
A death row inmate asks for Booth's help to prove his innocence before he is scheduled to be executed. Booth agrees and asks Brennan and her team to help him out.
Brennan is about to go out for dinner with her old professor and ex-lover when Booth asks her and her team to help identify the remains of a young woman found in a refrigerator.
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.
Brennan and Booth investigate the body parts of a woman found near L.A. International Airport. Their investigation is slowed due to extensive cosmetic surgery the victim had done.
When a woman’s burned body is found in a car with signs that her child was kidnapped, Brennan and Booth suspect the father, Carl Decker. But things get complicated when Decker turns out to be in the Witness Protection program.
Brennan and Booth investigate the origins of a decomposed body that's been found in a local alley and determine it's the remains of a shy teen with an alter ego.
Booth and Brennan investigate when a dug up corpse is found in the back of a gang member's car. While being questioned, a drive-by shooting allows him to escape. Booth and Brennan follow the clues, which lead them to an empty grave and another body in a grave at a wealthy senator's house, where the gang member used to work.
Brennan and Zach investigate a small jet crash that was carrying some Chinese diplomats and a woman. At the crash site, Brennan finds some bone fragments that do not belong to any of the passengers, but might belong to a man who has been missing for five years. Although ordered to work only on the diplomats, Brennan and her team go rogue to try to discover the identity of the extra bones.
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 stumble upon a subterranean world of homeless people when they find the remains of a filmmaker in the ventilation shaft of an underground tunnel.
While on vacation, Angela's boyfriend goes missing . When a skull shows up, she asks Brennan for help in identification, concerned it might be her boyfriend or the female guide who went missing with him. The investigation leads the team to a violent boyfriend, the local sheriff and ultimately to a counterfeiting ring setup in the desert.
The team helps Deputy Director Sam Cullen's daughter, Amy, when she contracts a rare form of lung cancer after receiving a bone graft. Booth and Brennan learn she is not the only victim with this rare form of cancer.
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.
A train carrying a popular Senator is derailed by a car positioned on the tracks. Brennan works out why the dead body of a rich businessman was placed in the car, and the search continues for her father. The team has a new boss.
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.
When the body of a young man, who's been missing for nearly three weeks, is discovered, the investigation leads them to his girlfriend, who is a foster child. Bones becomes emotionally involved in the case since, she too, became a foster child after her parents disappeared.
After digging up the skeletal remains of a young girl, the investigation points to a convicted serial killer on death row. The team follows cryptic clues that lead to another body, an accomplice, and a victim who may still be alive.
There are two suspects with the same motive when Booth and Brennan investigate the murder of a man found in a bathtub full of chemicals. They soon discover that he had two wives and a girlfriend.
The team investigates the death of a 10-year-old beauty pageant star. The other contestants, their parents, and their siblings all become possible suspects. Hodgins and Angela go on a date that actually goes well, despite what everyone else predicted.
When the skeletal remains of a federal prosecutor who disappeared five years earlier are found in the desert outside Las Vegas, the team suspects it to be tied to the mob. Booth and Brennan go undercover as Vegas high-rollers in an attempt to uncover the mystery, Booth risks his life.
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.
While investigating the death of a film student who was working on a documentary about the legend of a headless witch, who haunted woods in the 1700's, Brennan develops a strong bond with the victim's brother.
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.
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.
Brennan has to work with another agent while Booth needs to see a therapist. The duo investigate the death of a college freshman, who took part in a 'Girls Gone Wild' type of video.
Booth and Brennan investigate the death of Terence Bancroft, one of the Jeffersonian's major donors, found dead at his home. Hodgins' relationship with the wife of the deceased years earlier, compromises the case.
A broken water main uproots multiple coffins in an old graveyard. When the team is brought in to identify the bodies for re-interment, they discover a newer skeleton that should not be in the graveyard, which has not been used for 50 years.
When Angela draws the face of an old woman to go with the decomposed skeleton of someone much younger, they soon learn the victim had Progeria, an aging disease. Booth and Brennan investigate to discover who would want to kill such a fragile person. Meanwhile, Hodgins and Angela's walk down the aisle doesn't go as planned.
After a skull smashes into the windshield of a teenager's car, the investigation reveals the skull has been gnawed on by human teeth, which implies cannibalism and marks the beginning of the Widow's Son case. Meanwhile, Angela and Hodgins hire a private investigator to find her husband. Bones searches for Zach's replacement and the team gets a wonderful surprise.
Brennan and Booth investigate the death of a soccer mom who was blown up in her mini-van. They soon discover that the victim was part of a group of radicals from the 70's, adding several names to the list of possible suspects.
Things get kinky when Booth and Brennan follow murder clues that lead to a lodge used as an S&M retreat for "jockeys" and their "horses." Meanwhile, Angela tries hypnosis in an effort to figure out her elusive husband's name so she can finally divorce him.
When a body that appears to be cooked is discovered, the clues lead Booth and Bones to an organic farm co-op. Meanwhile, the two of them must meet with Lance Sweets, an FBI psychologist who must determine if they should continue to work together.
On Halloween, two mummified bodies are discovered and found to be people reported missing the past two Halloweens. When Booth and Bones learn about a missing girl, linked to the suspect of the previous murders, the race is on to save her life.
The team suspect their own colleagues after the burnt remains of an intern at the Jeffersonian are discovered. Meanwhile, Booth poses as Cam's boyfriend at her family get-together.
On the 20th anniversary, the Foothill High School, class of '87 alumni unearth the time capsule they buried to discover the remains of one of their classmates inside. Booth and Bones investigate the past lives of his classmates in an effort to discover the truth.
Booth and Brennan investigate a mall Santa named Kris Kringle who was found dead by two elves. A series of clues makes the murdered mall Santa seem like he's the real deal.
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.
All team members are working to identify the bones from a college athlete who suffered a lot of fractures. After the body is identified they talk to his sister and somebody who acted as a sort of an adviser for the deceased. Angela and Hodgins have an important talk. Zack is overwhelmed by having to reconstruct the crushed bones to form a skeleton.
A woman's car is run off the road and she is killed, but her baby miraculously survives the accident. Booth and Brennan go to the woman's hometown to try to find out who's responsible for running her car off the road. Bones, with help from Booth, takes care of the baby until the team finds out who killed the mother.
Brennan's father Max Keenan is on trial for the alleged murder of FBI Deputy Director Kirby. Everyone on the team, except for Brennan, is called as a witness for the prosecution during the trial. Brennan on the other hand is the forensics advisor for the defense, and she must rely on both her dedication to her family and her skill as an anthropologist to help free her father.
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.
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.
Season four begins all the way in England, with Booth speaking at Scotland Yard and Brennan guest-lecturing at the prestigious Oxford University. Knowing of Booth and Brennan's expertise in their respective fields, local officials ask for their help with a high-profile murder investigation that involves a British heiress.
The body of the host of a popular reality TV show is found partially decomposed in an outhouse, and Booth and Brennan must find out who the killer is. Meanwhile, Booth learns that Brennan is juggling two relationships.
Parker, Booth's son, discovers a corpse's finger in a bird's nest, causing the team to launch an investigation to try to find the rest of the body. After finding the corpse, the team discovers that the death was caused by a dog, leading them to an illegal dog fighting ring and a search for the killer dog and its owner.
The pieces of a dismembered body are found lying in a purple pool of water, except the head is missing. The team finds that the body belongs to Jared Addison, a science fiction writer who had several mental problems. With Sweets' help, several suspects are hunted down, however the team has trouble finding enough evidence with the victim's head still missing.
The remains of a despised office manager are discovered in an elevator shaft, and Booth and Brennan must figure out which employee killed him. After some investigating, they find that the manager had more than a fair share of complaints on file. Meanwhile, Angela and Hodgins try to make peace in the lab after their break-up.
Booth and Brennan go to investigate a body found in the Chesapeake Bay. After arriving, they find only the upper torso, giving the team little to work with other than remnants of the victim's breast implants. Brennan and Booth are led to a small church in Maryland, where they find that the victim was a pastor. When the team finds the lower half of the body, they learn that their initial assumptions may not been incorrect.
When the smashed remains of a well known artist are found in an impounded junkyard car, Booth and Brennan are on the case to find out if foul play is to blame for his death. With suspects ranging from the artist’s rival to his own assistant, the team must race
against the clock to find evidence of murder before the car is relinquished and put on exhibit as the sculptor’s ultimate display of self-sacrifice for the sake of his art.
Booth’s Brother Jared Booth and Brennan investigate the scene where a body was uncovered during a botched practice police raid. The team identifies the body as a struggling inventor’s father who had recently reunited with his son. But when a second body surfaces, the team is led on a trail of deception to find out who was the actual con-man in the inventor’s life. Clark Edison returns to the lab, and he and Hodgins work on piecing together blueprints from one of the inventor’s potentially valuable inventions.
Meanwhile, Brennan likes Booth's brother and goes out on a date with him. She learns a thing or too about Booth's past while out on the date.
While en route to China to identify prehistoric anthropological remains, Booth and Brennan are called upon to solve a murder in midair when the flight attendant discovers a fully cooked human body in the plane's microwave.
Brennan's father Max lands a teaching position at the Jeffersonian. When he ends up helping out with the murder case at hand, Brennan is noticeably bothered by his sudden presence in her professional life.
A shallow grave holds the remains of conjoined twins; Booth and Brennan infiltrate a circus community after they discover that the twins were jugglers there.
When a volunteer fireman is murdered at an ice rink, Booth and Brennan begin the investigation, but Booth must excuse himself due to a conflict of interest. When details come to light, Booth becomes a suspect in the homicide.
The team investigates a sci-fi convention when a woman in a medieval princess dress is found murdered. With Booth's back injured, Agent Payton Perotta steps in once again to help
When newlyweds encounter a corpse while bungee-jumping off of a bridge, Brennan and Booth are sent to investigate. After determine the cause of death was not suicide, the team at the Jeffersonian discover an unknown substance coming from the body. This sends the lab into lockdown and have only 24 hours to uncover the murderer before the body disintegrates.
The body of a pregnant 16-year-old athlete found buried in a mound of salt in a city de-icing truck leads Booth and Brennan to the discovery that many of her teammates are pregnant or have babies after a pregnancy pact.
When the half-eaten body of Cam's former fiancee is found in the tiger cage at the zoo, Booth and Brennan uncover that his death was far from accidental. Now the team must put the pieces of the fiancee's final day back together, including hypnotizing a suspect in order to spark his memory.
Booth and Brennan are sent to investigate when human remains are found during a photo shoot. When the team uncovers a meteorite in the victim's ear, they are led to the Collar Institute of Science in D.C.
When it is discovered that a stage prop used by a Norwegian death metal band is in fact a real human skeleton, the remains are sent to the Jeffersonian when authorities determine the victim was an American citizen.
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.
Booth's detective friend from Tokyo, Ken Nakamura, calls him when his sister, Sachi, goes missing while in Washington, D.C. With Brennan, Booth investigates her disappearance.
When a human body is found inside the strung up Otter mascot uniform of a rival school, Brennan and Booth investigate whether the body inside the costume was dead beforehand, or killed during a Middlesex University bonfire event. The body is identified as Jimmy “Beaver” Bouvier, a fraternity brother at Middlesex University. When Brennan and Booth question his fraternity brothers, they learn that Beaver had a money-making operation on the side and was making a killing of his own. Meanwhile, Booth offers to help his brother Jared find a new job after being dishonorably discharged from the Navy.
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.
In the season finale, a dead body is found at a club called "The Lab." The team has to do some unexpected and unusual things that have to do with this club. Brennan and Booth may become a couple.
It's been six weeks since Booth and Brennan have seen each other. Booth has been recovering from brain surgery, and Brennan has been on a dig in Guatemala. Angela's psychic, Avalon Harmonia reveals while reading Angela's tarot cards that there are multiple bodies buried under a Washington,DC fountain. Angela shares the information with Brennan and Booth, but they're both a little skeptical. The lead pans out, and the duo find the remains of 11 bodies exactly where the psychic said they would be. Meanwhile, Sweets has certified Booth mentally fit to return to duty after his brain surgery, but Booth is still experiencing some side effects from the coma.
Brennan and Booth are asked to investigate the death of a man who was murdered for the secret contents of his briefcase. They suspect that secret operatives are at work, and their theory is proven correct when they find the liquefied remains of a CIA agent in the trunk of a car. Meanwhile, Brennan's new best-selling book causes tension between her and Booth, and Wendell loses his scholarship.
When human remains are found alongside the railroad, Brennan and Booth are called to the case. The bones belong to Levi Yoder, a member of the Amish community who disappeared two months ago, during his Rumspringa, or exploration of the outside world. Brennan and Booth discover that Levi was a piano prodigy, and their investigation leads them to believe that his extraordinary talent may have lead him to an untimely death. Meanwhile, Cam copes with the stress that comes from being a new parent.
Brennan and Booth investigate human remains found at a neighborhood block party. Suburban politics and secret scandals give each neighbor in the cul-de-sac a motive, leaving Brennan, Booth and Sweets to sift through the drama to find their suspect. Meanwhile, Jeffersonian intern Arastoo comes clean about his background, and Booth's son attempts to find Booth a girlfriend.
Brennan and Booth are called to investigate what appears to be charred human remains on an electrical fence. The mysterious corpse is later determined to be a mummified Egyptian royal on loan to the Jeffersonian. The anthropological mystery has Brennan in a tizzy, and when the Jeffersonian curator prepping the mummy for exhibition is murdered, the team suspects foul play. Brennan’s investigation of the curator sheds new light on the life of the Egyptian royal, turning their case into one of historic proportions. Meanwhile, Brennan goes on a date with Booth’s supervisor and former intern, and Sweets’ girlfriend Daisy Wick (guest star Gallo) returns to the Jeffersonian.
Remains of a chicken farmer are found on the bank of a nearby river, and Booth and Brennan are called in to investigate. The farmer, who was an animal rights activist, was about to inherit a chicken factory and had many enemies with motive to kill him – leaving the team with a lot of murder suspects to sort through.
Stephen Fry returns as Dr. Gordon Wyatt. Booth, still suffering some lingering effects from his brain surgery, has to get re-certified for FBI marksmanship, but is not the accurate shot he was before going under the knife. He and Brennan investigate the death of a little person who was a former wrestling star.
Booth’s grandfather comes to live with him and tags along as Brennan and Booth investigate human remains that were found by a real estate agent while showing a property to prospective buyers.
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 a man dressed as Santa Claus blows himself up during a botched bank robbery, Brennan and Booth work to identify the bomber and determine his motives. Meanwhile, Brennan makes plans to spend Christmas in El Salvador, but her father convinces her to spend the holidays with him and Margaret Whitesell, a newly discovered distant relative.
Brennan and Booth travel to New Mexico to investigate human remains with extraterrestrial attributes. Meanwhile, Angela and intern Wendell come clean about their relationship.
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.
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.
Brennan and Booth investigate a set of uniquely disfigured remains allegorizing biblical text. As they acquire more information about the victim, a former patient of Dr. Adam Copeland at Havenhurst Sanitarium, they are confronted with suspects who are hard to characterize as either good or evil. Meanwhile, Jeffersonian intern Arastoo Vaziri reveals a secret about his past.
When a subway train is thrown off the track by 60,000 gallons of flood water, a partially skeletonized body emerges out of the overflow. While Dr. Sweets, a passenger on the derailed train, copes with post traumatic stress, the rest of the team and intern Daisy Wick get to work on identifying the victim as Martin Aragon, a professional ghost writer caught up in a deadly love triangle. Meanwhile, Brennan releases her second book to great success, but has to accommodate a nosy reporter, and Sweets' near-death experience leads him to make a drastic decision.
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.
The team’s latest case takes Brennan back to her alma mater, Burtonsville High School, where she and Booth investigate the discovery of an unidentified skull and upper torso. With Angela’s help, they identify the victim as one of Brennan’s classmates, and notice a possible connection to a second murder committed 15 years prior. Brennan and Booth go undercover as a married couple at her class reunion to interrogate a set of suspects, where even as an adult, Brennan is still predictably misunderstood and her only friend lies in a strangely dark and offbeat janitor. Meanwhile, Hodgins spills a lab secret
When human remains are discovered in the belly of a shark, Brennan and Booth are brought in to identify the missing person. Evidence suggesting the victim had been the prey of several fish directs the team’s investigation to The Aquarium of the Atlantic, where a guest lecturer and notorious self-help guru preaching the healing power of the ocean has gone missing. Meanwhile, both Brennan and Booth navigate their own relationship when a marine biologist shows interest in Booth.
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
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.
With Cam’s reputation and career on the line, the team travels from overseas to help her solve the case of an unidentified young boy. The Forensics Anthropology Unit lost much of its vigor after disbanding to pursue personal ventures, and it will take the collaborative energy and knowledge of the newly reunited team to unravel evidence and find closure for the family of the unknown boy. After unearthing new clues in the lab and making unexpected personal discoveries, the team realizes they belong back in Washington, D.C.
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 Booth and Brennan are called to investigate decomposed remains found at the Jersey Shore, the team IDs the victim as Richie “The V” Genaro, a 23-year-old who partied the night before at a popular nightclub. Booth and Brennan question Genaro’s peers and the club bouncer, and Brennan surprisingly proves her pop culture savvy and anthropological expertise after watching what she believes to be a documentary on the inhabitants of the Jersey Shore, but was in actuality a reality show set there. Meanwhile, at the lab, the team grows fond of Booth’s girlfriend, Hannah, and Angela tries to keep her pregnancy a secret.
After a skull and decomposing hands are found in a dumpster, the team must not only solve the crime but also search for the rest of the victim’s remains. Identified as Ray Raminsky, the victim turns out to be a bounty hunter in search of Charles Braverman, a man indicted for the murder of a co-worker. Meanwhile, Brennan is asked by Professor Bunsen Jude “The Science Dude” (guest star Grier) if he can shoot an episode of his children’s show from The Jeffersonian Lab with Brennan as his special guest. Brennan initially turns him down, but is surprised when he makes her a deal she can’t refuse, so she takes him on as a new “squintern.” As the team pieces together the details of the crime, they discover that they are not alone in the hunt for Braverman and find themselves in a chase with an unexpected suspect.
After the skull of a promising young dancer is found lodged in concrete at a construction site, the team must first figure out what happened to the victim’s skeletal structure. After learning the victim quit ballet to pursue hip hop, Booth and Brennan uncover another layer of evidence that points them to a suspect who had a secret relationship with the victim. Meanwhile, when Hannah is put on assignment in a dodgy part of town, her safety is jeopardized and her life is put in critical danger.
The past and present collide when human remains from a 150-year-old slave ship, the Amelia Rose, surface. The team is tasked to give the deceased a proper burial but make an unforeseen discovery linked to a recent murder. In the course of the investigation, Booth and Brennan are led to a different kind of ship - a "Cougar" cruise - where they learn their victim was seen moments before his death. Meanwhile, Sweets struggles to maintain a casual relationship with Daisy, and Cam discovers a surprising and emotional connection to the Amelia Rose.
An event for a candymaker (Wayne Knight) turns bitter when human remains are discovered in the world's largest chocolate bar; Cam struggles with her daughter's decision to attend a college that fails to meet her high standards.
Booth and Brennan’s next case leads them to a crime scene where a human carcass has literally melted into the dashboard of a charred truck. As the team investigates the case, they discover a gunshot wound in the victim, but learn that neither the fire nor the bullet was the cause of the victim’s death. Additional clues lead them to a local high school where the victim’s wife is a teacher. As a student-teacher relationship begins to surface and a pattern takes shape in the lab, the team is able to track down the murder weapon and solve the crime. Meanwhile, Sweets resists the temptation of allowing his feelings for Daisy to interfere with helping her pass a government psychological evaluation, and Hannah attempts to break the ice and warm up to Booth’s son Parker.
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.
An unidentifiable body is discovered in the shower of an upscale home belonging to a young female socialite. With the help of nosey bones expert and Jeffersonian “squint” Clark Edison, skeletal reconstruction and evidence in the drain reveal that the victim was a young girl employed by a counterfeit handbag distributor. The team learns that the victim supplied counterfeit purses to her socialite acquaintance, and after interrogating the self-centered socialite and sifting through footage on a hidden camera, they discover evidence linking them to the murderer. Meanwhile, Angela and Hodgins discuss their future home and where they want to raise a family, and Booth opens up to Hannah about Brennan’s feelings for him
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.
A body disguised as a scarecrow is found with a bullet wound in a remote cornfield, and the team is forced to work against the clock to avoid a storm and potential complications that would affect the evidence. Booth and Brennan interrogate the victim's three wives, who are also sisters, and learn that jealousy between the sisters and their desire for their husband's attention had caused a major rift in the family. Booth and Brennan also question one relative who disapproved of the victim's polygamy. Meanwhile, Cam loses confidence in her relationship with her on-call doctor boyfriend, but they both realize they need to make their relationship a priority.
A BMX rider’s remains are discovered on the roof of a warehouse after a failed bike stunt. While Booth and Brennan interrogate the victim’s fellow riders, Hodgins and newly mellowed “squint” Fisher identify the numerous fractures in the victim’s skeletal structure, and Angela recreates the series of events that led to the fatal accident. Meanwhile, Sweets turns to Booth for advice about his relationship with Daisy, and Booth makes a decision about his relationship with Hannah.
The liquefied remains of a wedding planner are found in her home tanning bed on Valentine’s Day, and Cam pressures her team to solve the case in time so she can celebrate the holiday with her boyfriend. While the “squints” works tirelessly in the lab, Booth and Brennan interrogate a slew of possible suspects until they unlock classified files in the victim’s computer, which lead to their main suspect. Meanwhile, Booth and Brennan downplay the significance of Valentine’s Day, and Hodgins tries to plan a romantic day for Angela, but “squint” Clark helps him realize that the most meaningful gifts come from the heart.
Sniper Jacob Broadsky takes out a victim who escaped from the justice system; Booth uses his military training to try to stop Broadsky before he strikes again; Angela's father visits the Jeffersonian.
During a blizzard that causes a citywide blackout, the team must solve a murder case that could be connected to a possible viral outbreak; Sweets starts a touchy conversation about Brennan and Booth's relationship.
Brennan teams up with a Canadian forensic podiatrist to determine the real victim after eight pairs of feet are found washed up on the U.S.-Canadian border, but seven pair belong to research. Elsewhere, Cam crosses a major boundary when she takes away Michelle's right to choose her own college.
The remains of a mythbuster television show host are found in the wilderness appearing to have been killed by the mythic Chupacabra, a reptile-mammal hybrid creature whose existence has not been confirmed. The team soon learns that the victim traveled to the remote West Virginian area to debunk the Chupacabra myth, and they interrogate possible suspects, including a rival wilderness-channel host/cryptozoologist/pet psychic. But when a tape is recovered at the crime scene and peculiar tooth marks are found in the victim's remains, the team learns details about the victim's demise that challenge the original theories surrounding his death. Meanwhile, recovering alcoholic squint Vincent Nigel-Murray makes amends with each member of the team and makes some surprising confessions.
The remains of a maritime museum security guard are found in the Florida Everglades after an attempt to steal an obsolete 17th century nautical chart fragment used to find treasures. In order to solve the crime, Booth seeks out Walter Sherman, a former Iraqi soldier with an uncanny gift to unearth anyone and anything. With Sherman's help, as well as that of his colleague, Ike Latulippe, and his legal advisor, Leo Knox, the team is led to tattoo artist who points them in the direction of a tough young woman. But when the woman is found murdered with remnants of the map lodged in her remains, the team discovers centuries of history linked to the map and the suspect behind the crimes. Meanwhile, Brennan puts Sherman's remarkable skill to the test, and Booth harbors cold feelings toward his former military comrade.
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
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.
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.
The discovery of the CEO of a toy company packaged with his toys gives Booth and Sweets access to the company's headquarters as they search for the murderer. Elsewhere, Brennan is concerned about her fitness as a mother and Sweets is concerned about his gun certification test.
Dismembered remains are discovered in several mailing boxes at a dead letter office, and the Jeffersonian team identifies the victim as an employee of a local Ship 'n' Print, where the staff recently split the winnings of a lottery prize. The team uncovers a complicated love triangle between two married employees and the victim, and while motive points to the husband a critical clue leads them to solve the crime definitively.
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.
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.
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 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 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 a corpse is found in the middle of the woods, the team links the victim to two families that have been feuding for almost a century. Brennan and Booth interrogate a family member with a shocking confession that leads them to a motive for the victim’s murder. Meanwhile, Brennan has a difficult time accepting her father’s offer to babysit their infant daughter because of his unpredictable presence in her own childhood.
A film adaptation of Brennan's latest book takes her and Booth to Los Angeles for the production, where Brennan criticizes the acting and disregard for science, but the trip takes a strange turn when a prop cadaver happens to be a real murder victim.
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.
The Jeffersonian team investigates the murder of a high-powered divorce lawyer with a lot of enemies. The plot thickens when the team discovers that the attorney's wife and assistant have been hiding crucial evidence which could help solve the case. Meanwhile, Brennan tries to adjust to life after being on the run, and tensions start to rise between her and Booth as the impact of their three-month separation begins to take its toll.
An investigation of human remains found in the aftermath of an explosion in a hotel garage hits a snag when the team learn their assumptions about a man's fate are incorrect. Meanwhile, Sweets gets a temporary partner at the FBI.
The team's investigation of the death of an animal expo worker leads them into the shady market for illegal animal trading. Meanwhile, Brennan considers her political aspirations; and Sweets and Daisy confront a change in their relationship.
The Jeffersonian team investigates the death of a woman whose body was found mutilated and discarded in a city garbage can. Meanwhile, Booth invites Sweets to stay with Brennan and him while Sweets searches for a new apartment.
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.
The remains of a crime scene cleanup expert are found sealed in a mysterious pod that washed up on a beach. Meanwhile, Angela and Hodgins have reason to believe that Cam has a secret lover.
A street artist who is plastering his work on a billboard falls into his glue—and onto a corpse—so the team try to get him unstuck from the remains as they also work to identify the body. Meanwhile, Booth takes a stab at stand-up comedy at a club's open-mike night to look for suspects; and Angela finds herself attracted to the street artist.
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.
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 team investigates the murder of a well-known archaeologist with a questionable reputation, who came upon a career-defining discovery right before his death.
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 remains of two bodies that were found at the same burial plot: one of a female cancer patient; the other, the cancer patient's "doula," who was guiding her through her grieving process with the illness. Meanwhile, with a spotlight on the case, Brennan and Booth start discussing their individual choices for after-death arrangements. Also, Daisy Wick returns for her first case after her break-up with Sweets.
The dismembered body of a roller derby skater means Angela goes undercover at the rink to find more clues to the woman's murder. Elsewhere, Cam worries over the sheer number of doctor appointments Booth is going to, and presses him for details.
When Brennan is shot while working late at the Jeffersonian lab, she is rushed to the hospital in critical condition. While at the hospital, she struggles with visions of her mother that defy her usual logic. Meanwhile all evidence suggests that Brennan's attacker may be linked to the Jeffersonian.
The Jeffersonian team investigates the remains of a 15-year-old boy. Although his mother and few close friends saw him as intelligent with poor social skills, the team discovers that this seemingly innocent boy was actually involved in illegal activity and had attended a high school party two weeks prior where drugs were present. The investigation takes an ugly turn when an underage girl confesses to being raped and the deceased boy’s reputation is compromised. Meanwhile, with the case’s spotlight on deception, intern Finn Abernathy contemplates telling Cam that her daughter Michelle is in town visiting for the weekend.
When extremely educated new intern Dr. Oliver Wells (Brian Klugman) starts working at the Jeffersonian, his quick-learning, enthusiastic personality challenges Brennan as he gets under her skin with his eccentric but undeniable observations, causing her to try to be more open-minded about many scientific questions. Meanwhile, Booth worries she may have gone too far when she accepts the possibility of time travel as a factor in a murder investigation.
The Jeffersonian team investigates the death of Symchay Conteh, a young man whose remains were found in a barrel at a hazardous waste disposal facility. They discover that the victim was an immigrant from Sierra Leone working numerous part-time jobs in order to make ends meet. Meanwhile, as the team gets deeper into the investigation, Cam and Arastoo find it even more difficult to keep their relationship a secret and Brennan and Booth try to decide on a vacation destination.
When the Jeffersonian team investigates the death of a former Marine sergeant whose remains were found burned to a crisp, they discover that she was discharged after a fist fight with another Marine. When Booth and Sweets go to question the other Marine involved in the altercation, they learn that Deanna was obsessed with the idea of the apocalypse, which leads the team to a following of doomsday preppers who become key suspects in her death. Meanwhile, Sweets thinks he has landed his dream apartment but Brennan and Booth are not convinced that he will actually move out.
An undercover police officer, who was investigating a string of ATM robberies, turns up dead in a van with a bag of diamonds found inside his mutilated body. So the Jeffersonian team must figure out whether or not the ATM robbers are also murderers, or if the cop was crooked. Meanwhile, Brennan is the subject of a documentary commissioned to raise funds for the Jeffersonian, and she struggles to be likeable on camera.
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 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 Jeffersonian team rushes to prevent a viral outbreak while investigating the murder of journalist Mia Garrett after her infected body is found at a biohazard facility. When the mutated virus that killed Mia infects Jeffersonian intern Arastoo Vaziri, their only chance of saving him is by solving the murder. Tension and passion build as the team races against the clock to find the killer - and the cure.
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.
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 Jeffersonian team investigates the murder of Adam Pak, a management consultant whose remains were found being eaten by bobcats. When evidence leads the team to a marriage retreat site, Brennan and Booth go undercover as previous personas "Roxie" and "Tony" to try to find more evidence. While at the retreat, Brennan and Booth meet fellow married couple Bill and Evelyn Schumacher, whose relationship seems a little too perfect.
The Jeffersonian team investigates the murder of Jamie Delcampo, a member of the Estrellas Locas gang, whose remains were found in a burnt out car. Meanwhile, having taken time off from the FBI in the wake of Pelant's latest assault on the team, Sweets ultimately decides to help with the investigation when he discovers that a young boy from the center where he volunteers is the son of one of the gang members.
The team investigates the murder of a high school principal who was dying of cancer; Brennan and Booth plan their wedding; a virtual profiling system threatens Sweets' job.
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.
Unable to relax on their honeymoon, Booth and Brennan decide to help a local detective solve the murder of a Nazi war criminal; Hodgins and Angela look after Christine.
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 Jeffersonian team investigates the murder of a food scientist whose remains were tossed in a meat grinder and mixed into cans of stew served in a school cafeteria. When the team uncovers the scientist's newest - and highly lucrative - food invention, they also track the trail of jealous competitors in the multi-million dollar food industry. Meanwhile, Angela plans a post-wedding bachelorette party for Brennan, which gets crazier than intended.
The Jeffersonian team investigates the murder of a nationally ranked gymnast, whose remains were hit by lightning and scattered throughout a public park. Although evidence points to a fellow gymnast as the key suspect, Brennan and Booth discover the victim was leading a double life. Meanwhile, Booth gets upset when Brennan shows surprising empathy for the victim's father, and Cam confronts the woman who stole her identity.
The Jeffersonian team investigates the death of Colin Haynes, a struggling country music singer whose remains were found in a shallow grave. When the team learns about the victim's music career, it leads them to his record label, which, they discover, was deceitful in its dealings with him. Meanwhile, squintern Wendall Bray breaks his arm during a hockey game and Brennan takes a closer look at his injuries, only to discover some shocking news.
When the team discovers a renowned chess master in pig slop, Sweets goes under cover in the chess world; a science magazine honors Cam; Dr. Douglas Filmore fills in as lab intern.
The Jeffersonian team investigates the murder of Lauren Frank, a kidnap victim whose remains were found buried at a park. But when they discover the unhappy relationship that Lauren had with her stepmother, the team starts to think the killer was someone closer to the girl than expected. Meanwhile, Hodgins uncovers a shocking secret about his family and Brennan and Booth face a common couples dilemma - whether to co-mingle their funds.
When a CIA informant is found murdered, Booth and CIA Agent Danny Beck (guest star Freddie Prinze Jr.) must work together to track down an Afghani terrorist. Meanwhile, Brennan wants to work more closely with Booth in the field, and the duo must confront the implications of what that means to their family.
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.
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 a wealthy artifact collector walks into his own funeral, the team must determine the real identity of the deceased; Finn's new hot sauce venture is making big money.
The remains of a former art student are found in a log in a forest; Wendell returns after beginning cancer treatments; Booth prepares for an FBI competency test.
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.
When the remains of a woman from a wealthy family are found in a national park, the team thinks she may be a victim of the Ghost Killer; Booth's career might be in for some changes.
When the head swim coach of a community college is found dead at the bottom of the well, possible suspects think he may have been having an affair; Sweets covers for Booth in the investigation as Booth prepares for a congressional subcommittee.
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.
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.
The remains of a right-wing radio host are found in a storm drain, and the investigation reveals some surprising extracurricular activities that narrows the search for suspects. Meanwhile, Agent Aubrey tries to get Booth to trust him, and Brennan worries about her husband's state of mind.
The investigation of the murder of a video-game designer reveals the wealth he accumulated during his career, which makes a suspect out of everyone who was in his inner circle. Meanwhile, "squintern" Jessica sheds light on an educational opportunity; and Brennan and Booth discuss Christine's future.
Brennan runs into a publishing rival. Wendell hears back from his diagnosis. The team members investigate a murder when remains are found in a convention's stairwell.
Paying homage to Alfred Hitchcock in an episode that reimagines the Jeffersonian and FBI teams in 1950s Hollywood. Brennan plays an LAPD detective who's battling sexism on the force, and Booth is a notorious jewel thief who is far more than he seems to be. When Booth is framed for the murder of a rich socialite, he and Brennan team up to clear his name and find the true identity of the murderer.
When the Jeffersonian team discovers remains of a victim, and elements of the crime scene point to a possible protege of serial killer Christopher Pelant, they must revisit their prior work on Pelant while tracing new clues that will hopefully lead them to the copycat killer. Meanwhile, Angela is skeptical about her and Hodgins decision to move to Paris and Brennan and Booth contemplate options outside of the Jeffersonian and FBI.
Booth goes missing six months after he and Brennan left their careers behind, but a case with ties to the couple pulls Brennan back into the world of forensic analysis, which brings her into contact with a member of Booth's family and Arastoo Vaziri, who's taken the lead at the Jeffersonian in her absence. Meanwhile, the FBI investigate Booth's disappearance, but one agent's tactics are bad for the team's morale.
Booth is still missing, but the team learns that Agent Miller has hidden information about his whereabouts and physical state. Meanwhile, a digital forensic scientist helps Angela try to decipher information pertaining to Booth's location and the circumstances of his disappearance; and Arastoo makes a decision that will change his and Cam's personal and professional relationships.
On Brennan and Booth’s first official day back at their respective positions at the Jeffersonian and the FBI, things get exciting when remains are found at a fish farm under suspicious conditions, prompting them to investigate. After it’s discovered that someone harvested several of the victim’s internal organs before he was dumped in the water, Angela tracks down the seller and buyer of the organs to try to uncover important details in the case. Meanwhile, Booth readjusts to his position back at the FBI and discovers Aubrey has taken over his old office; Hodgins pushes Angela to showcase her photography work; and Cam struggles with her decision to choose work over her relationship with Arastoo.
When remains of real estate agent Justin Ross are discovered in a forest and appear to have been destroyed by coyote-wolf hybrids, Brennan enlists the help of fellow brilliant forensic anthropologist Dr. Beth Mayer to assist in the investigation. In addition to her professional achievements, Mayer is surprisingly knowledgeable about the world of fantasy football, a key link to Ross’ past and one that could provide vital information in finding his killer. As Booth and Aubrey dig into Ross’ fantasy football league history, they discover he was actively involved in a Twitter feud with NFL star Lou Divers, and was also owed a large sum of money from the league’s commissioner, making each of them suspects. Meanwhile, Brennan resists feeling competitive as Mayer impresses the team with her expertise and decades of accomplishments.
It’s Halloween time at The Jeffersonian as the team gets a surprise visit from Lt. Abbie Mills and Ichabod Crane, who have traveled from the spooky town of Sleepy Hollow to help on a murder case of a young woman whose body is found on top of a 18th century military general’s headless body. The new foursome must figure out how to work together to discover who the 200-year-old headless corpse is and how the two murders are linked. Meanwhile, Booth and Brennan come up with the ultimate Halloween pranks to play on each other.
The crossover continues on Sleepy Hollow S03E05 Dead Men Tell No Tales (II).
A pair of funny sanitation workers discover the shredded body of a U.S. Senator in a street sweeper, which leads Brennan, Booth and the team to Capitol Hill, where they meet with U.S. Senator and majority whip Hayley Winters and the victim's chief of staff Eric Morales to get to the bottom of this political murder. Meanwhile, as Aubrey starts to develop a relationship with squintern Jessica, he looks into her past to make sure nothing will harm his dream of a future in politics
The team investigates the murder of an escape artist whose body is found in the woods. They discover that the victim worked at the Magic Palace, and had some secret activities in the works that might have made him enemies in the magic community. Meanwhile, Brennan and Booth poll their friends as to whether or not the tooth fairy should visit Christine, and Angela continues to work with Sebastian Kohl on her photography.
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.
Hodgins is eight weeks into his rehabilitation for his paralysis and forced to navigate life in a wheelchair. Meanwhile, Brennan and Booth investigate the death of a public defender who had multiple defendants from previous cases with motives to kill her.
The team investigates a body found in a car crash, the remains of which belong to a founder of a men's rights organization who may have been the victim of domestic abuse. As Brennan learns more about the tenets of the victim's organization, which claims middle-aged white men are oppressed and feminists are man-haters, Brennan uncharacteristically loses her cool during an interrogation and assaults the organization's co-founder. Meanwhile, Angela and the team struggle to deal with Hodgins post-wheelchair bitterness and Booth is convinced Brennan is a jinx for the Philadelphia Flyers.
The Jeffersonian investigates the decomposing body of a social worker in the park, but evidence suggests the killer lived with the body for months before dumping it. Things get even more complicated when they determine another set of remains has similar details, which link the victims to a serial murderer who had sinister interactions with his victims' bodies. Booth and Aubrey consult with behavioral analyst Karen Delfs to help with clues to the killer's identity, while Cam tries to determine what (and who) she wants in her romantic life.
The Jeffersonian investigates the murder of a convicted felon who had been released to a halfway house, but disappeared, and a suspect in the case has ties to Booth. Meanwhile, Brennan testifies at an FBI hearing about the circumstances regarding her assault of an unarmed suspect from a previous case, and the outcome of the hearing could lead to her suspension and prevent her from working with the FBI. Aubrey and Jessica’s first kiss is delayed again and Hodgins continues to push Angela away.
The team investigates the body of a private investigator who was found frozen in ice, after being dumped in the Potomac. The victim, a man with many enemies, was a "fixer" who made sure his clients' problems got "resolved." Meanwhile, Aubrey is shocked to find information tied to his father's whereabouts, Angela and Hodgins continue to work on their rocky relationship, Brennan and Booth get Christine's first report card and criminal behaviorist Karen Delfs asks Aubrey out on a date.
The team investigates the death of the leader of the Lynwood University male acapella singing group, "The Whippersnaps," whose body was found in the school rat lab. The victim recently kicked out Ian Jansen, one of the group's best singers, sending Booth and Aubrey to question Ian and other current members of the male group and some stars of the competing female acapella group to get a handle on the group dynamics and what could have led to the murder of one of their own. Meanwhile, surprising information about Aubrey's own college experience is brought to light, Hodgins applies for an experimental nerve regeneration study, Booth tries to plan a summer trip with Parker and a new intern joins the Jeffersonian lab.
A drunk college student discovers the dead body of a Secret Service agent just before a presidential visit to the area. Booth is ready to hit the ground running and turns to Secret Service agent and former colleague Brandt Walker for information, but is surprised to learn the Secret Service has reservations about Booth’s involvement in the case. The team uncovers some shocking evidence that heightens the seriousness of the case, causing Booth to step up for his country. Meanwhile, Brennan is out sick with the flu and former intern Dr. Colin Fisher returns to the Jeffersonian to run lead on the case, but Brennan refuses to be kept out of the loop. Also, Hodgins takes his life into his own hands and turns a corner after a potentially dangerous experiment.
To produce a television segment on the Jeffersonian’s Medico-Legal lab, a documentary crew follows Brennan, Booth and the Jeffersonian/FBI team on a “typical” case as they investigate a corpse found in a landfill that was buried there more than a decade ago. The camera captures normally unseen footage of the team at work, while candid commentary by each of the team members provides an inside look at the investigation as Booth and Aubrey show off their unique skills in the field, and Brennan and her team prove their expertise and integral importance to solving murder cases.
The team investigates the death of a popular professional hockey player whose headless corpse was dumped in the river. As Booth and Aubrey question the player's coach, Booth's depth of hockey knowledge is integral to solving the case, and he's reunited with a hockey rival from his past, putting him back on the ice once again to face off against him. Meanwhile, Hodgins and Oliver have a competition of their own when Hodgins builds two drones and they compete to retrieve the victim's missing head, and Booth and Brennan attempt to declutter their home.
When the remains of famous billionaire explorer Henry Charles are found in Antarctica, the high profile case is brought to Brennan and Booth to determine if his death was a murder. The Jeffersonian team confirms he was killed when he went missing ten years ago on an expedition, but the timeframe puts the Jeffersonian's Dr. Clark Edison, who was with Charles for the expedition, on the short list of suspects. Meanwhile, Cam's sister comes into town to help with wedding plans and old family friction comes into the picture.
The team investigates a body found at a glass recycling plant with a diamond lodged in its jaw. French Inspector Rousseau approaches the team with an accusation against the Marquis De Chaussin, who is revealed to be the victim's husband and lives in Virginia. Meanwhile, Booth discovers he suffers from a temporary eye illness, and Hodgins thinks he's being followed by a ghost.
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.
Booth and the rest of the lab desperately search for Brennan who was kidnapped by her former assistant, Zack Addy. Brennan's rescue is, however, just the beginning of their problems.
After discovering the body of a man involved with creating artificial intelligence bots, the team must figure out whether the victim's own A.I. bot was programmed to kill him. In the meantime, Bones plans a special surprise for everyone for her 40th birthday.
When the body of an old man is found in an acid dump site, the team becomes enmeshed in retirement home drama. As they explore the case, talk of marriage and kids begins to dominate the conversation back at the lab.
The team investigates the murder of someone from Booth and Brennan's past. Meanwhile, Aubrey faces a moral dilemma of his own when he discovers his dad is back in the picture.
When a tutor of privileged students turns up dead, the team sorts through all the possible perpetrators, from disgruntled parents to the tutor's roommate with a criminal record. Meanwhile, Bones is frustrated with the voice of her audio book and tries to prove that she can record it herself.
The dismembered body of successful golfer-turned-lumberjack Phyllis Paul brings the squints to the Lumber Sports Regional Championships. At this competition, Booth and Brennan discover numerous secrets that could have resulted in Phyllis' murder, including an affair with a married rival. Meanwhile, Hodgins secretly analyzes the bacteria on the bone of a prior victim that he believes will exonerate Zack.
When a series of corpses with ties to Booth's former Army unit appear around D.C., Booth must dive into his past to find the killer before the killer finds Booth. Meanwhile, Brennan's father, Max, hides a serious medical procedure from Brennan, leaving her to grapple with her father's trust and mortality, as well as her family being in danger.
A recent loss creates a rift between Booth and Brennan, as they deal with their grief in different ways. Meanwhile, an old flame from Brennan's past comes to visit.
When a young man dies in a horrendous hay baler accident, Booth, Brennan and Aubrey slap on trashy disguises and go undercover at a rowdy demolition derby competition to investigate the case. Meanwhile, Dr. Gordon Wyatt returns and assists Hodgins and Cam when the ongoing Gormogon case hits a dead end.
When the burning, bruised body of an aspiring writer/director crash-lands onto a passing car, the team investigates a series of odd locations and characters that are connected to his film. Meanwhile, Bones seeks guidance from Dr. Mayer on the meaning of passion in the work place and Booth allows Aubrey to take the reins on their current case.
Brennan testifies for Zach in trial, Angela reveals some big news, while Aubrey and Jessica come to terms about their future together. All the while, the team discovers Kovac has escaped, leaving Booth in a race against the clock to protect himself and those closest to him from what may be Kovac's most dangerous plan yet.
With Kovac still at large, the team searches for evidence to track him down. After Brennan experiences a setback, the rest of the team must figure out how to find Kovac without her, putting everything she has ever taught them to the test. When all signs point to Kovac having outside help, as well as a hideout, Booth and Brennan go searching for him.
