F.B.I. Agent Seeley Booth is teamed up with forensic anthropologist Dr. Temperance "Bones" Brennan to solve some of the most baffling and bizarre crimes ever. Booth depends on clues from the living, witnesses and suspects, while Brennan gathers evidence from the dead, relying on her uncanny ability to read clues left behind in the bones of the victims.
Brennan has been kidnapped by her former assistant, Zack Addy, as Booth and the rest of the lab desperately search for her.
After discovering the body of a man involved with creating artificial intelligence bots, the team must figure out if the victim’s own artificial intelligent bot was programmed to kill him.
When the body of an old man is found inside an acid dump site, Booth, Brennan and the squints find themselves deep in retirement home drama.
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 the murderer, Zack Addy.
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.
In the series' penultimate episode, each leading character's final story begins to unfold. 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.
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 a man is killed driving an SUV registered to a Middle Eastern man, Dr. Brennan and her team find themselves tracking a terrorist.
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.
Brennan and Booth travel to Washington to investigate a human arm that was found in the stomach of a black bear.
Booth asks Brennan to help locate and identify the remains of a six-year-old boy, Charlie, who went missing from a local park.
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.
A human finger bone found in the clutches of a drowning victim leads to a search for buried treasure.
A trip to New Orleans leaves Bones beaten, bloodied, and suspected of murder while plunged into the world of voodoo.
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 and Booth investigate an apparent suicide in Arlington National Cemetery, but soon discover it is a murder linked to a military cover-up.
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 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.
Six months after the events of last season, Booth, Brennan, daughter Christine and the new baby are seemingly living a dream life, a world away from the murder-filled life they left behind. But a case with close personal ties to the couple forces Brennan to become involved in the forensic analysis of the remains, and Booth mysteriously goes missing, prompting an FBI investigation into his whereabouts led by Agent Grace Miller, who works closely with FBI Agent James Aubrey on the case. However, tensions rise when Miller tries to investigate one of the team’s own as the primary suspect. The case also brings Brennan into contact with a member of Booth’s family , and “squintern” Arastoo Vaziri, who has been filling in as lead forensic anthropologist during Brennan’s absence, hopes the temporary position becomes permanent
Another layer is added to the mystery of Booth's whereabouts and the state of his physical condition when the team discovers that FBI Agent Miller has not been entirely truthful with the FBI and the Jeffersonian, keeping vital information from them that could lead them to Booth. Meanwhile, the Jeffersonian gets a surprise visitor, FBI digital forensic scientist Dr. Benjamin Metzger, who works with Angela to try to decode the information the team has been able to uncover regarding Booth's location and the circumstances surrounding his disappearance. Also, Arastoo makes a major decision that affects his and Cam's personal and professional relationship
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. Crossover episode with Sleepy Hollow Season 3, Episode 5.
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.
To solve a murder, Brennan and Booth go undercover at an Old West-style shooting competition, while Angela and Hodgins discuss the future of their family and Cam gets close with photographer Sebastian Kohl.
The team investigates the murder of a police officer that sends shockwaves through both the Jeffersonian and FBI teams. Behavioral analyst Leslie Green is assigned to work with Booth on the investigation and lends her professional assessments on who the cop killer could be, while Cam must make some decisions in her personal life and the entire team re-evaluates what is truly important to them.
Hodgins is eight weeks into his rehabilitation 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, and the remains 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 multiple 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 cllients’ 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. 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.
Bones and Booth investigate the death of a professional hockey player whose headless corpse was dumped in a river. Booth is reunited with a hockey rival from his past, putting him back on the ice. 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.
The Jeffersonian and FBI investigates when the remains of famous billionaire explorer Henry Charles are found in Antarctica. The team confirms he was killed when he went missing ten years ago, but the timeframe puts Dr. Clark Edison on the short list of suspects. Meanwhile, Cam's sister comes arrives to help with wedding plans.
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.
When the body of a well-known cookie jar collector is found in a riverbank, the Jeffersonian team must submerge themselves into the victim's collector community in order to catch the murderer. Meanwhile, Booth struggles to come to terms with Brennan's decision that he move out of their house due to his gambling addiction and Aubrey has his eye on one of the "squinterns".
When the remains of an ex-con and biker gang member-turned-yoga instructor is found in the aftermath of a forest fire, the team must navigate both worlds from the victim’s past to find the killer. Meanwhile, Booth continues working hard to beat his gambling addiction and regain Brennan's trust, and Angela and Hodgins make a big decision that will impact their future at the Jeffersonian.
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.
Evidence points to Dr. Hodgins as the suspect when the Jeffersonian team investigates a murder that occurs during a forensic science convention they are all attending.
The Jeffersonian team investigates the murder of an immigrant maid whose remains were found on the side of the road.
After severely damaged human remains are discovered under a merry-go-round, the Jeffersonian team begins a complicated investigation of a billion dollar hedge fund company.
The Jeffersonian team investigates the death of a crossword puzzle genius whose body is found at a fracking site. Meanwhile, the team welcomes a new addition.
It is discovered that a college psychology professor has been conducting controversial social experiments on his grad students after his various body parts are found in dumpsters throughout the city. With Booth occupied by an online traffic school course, Brennan teams up with Aubrey to investigate the murder.
This homage to Alfred Hitchcock finds the Jeffersonian and FBI teams in a 1950s-styled Hollywood setting with Brennan as an LAPD detective battling sexism within the police force and Booth as a notorious jewel thief who is framed for the murder of a rich socialite.
The Jeffersonian team, with the help of Angela’s psychic friend, Avalon Harmonia (guest star Cyndi Lauper), is drawn into the twisted world of fortune tellers when the body of a local psychic is found decomposing in the trunk of a tree. However, when the team learns more about the victim’s personal life, those closest to her become suspects. Meanwhile, Booth and Brennan debate the pros and cons of Christine’s new imaginary friend and the team remembers Sweets on his birthday.
When the remains of a high-stakes gambler are found in an industrial shredder, Booth risks relapsing into his gambling addiction as he and Brennan delve into the world of underground poker. Meanwhile, Hodgins invents a new product related to the lab, and Brennan and Booth find out some exciting news.
The Jeffersonian team works diligently to get Booth out of jail and absolve him of crimes he did not commit. Meanwhile, Daisy and Sweets have a surprise for the rest of the Jeffersonian team.
The Jeffersonian team investigate the murder of a controversial conservative radio shock jock who had some interesting extracurricular activities. Meanwhile, Brennan is concerned about Booth's psychological well-being in light of recent events.
The murder of a video game designer leads to numerous suspects after the team uncovers information about how he acquired his fortune.
The body of a popular TV celebrity chef are discovered at a local park, and the Jeffersonian team must search for clues in local restaurants that he had been reviewing. When evidence points to the Royal Diner, Brennan and Booth’s favorite eatery, the two must risk their status as favored patrons by questioning the staff. Meanwhile, Hodgins sells his new invention for millions and Brennan creates an anatomically correct song to help Christine learn about the bones in the human body.
When the remains of a private high school student are discovered in a ditch, Brennan and Booth surmise that bullying was a factor. When Brennan discovers similarities between her own teen years and the victim’s, it leads the team to question whether or not the girl’s death was, in fact, a murder.
With only 48 hours before the execution of serial killer Alex Rockwell, whom Brennan and Booth helped convict, the Jeffersonian team must race against the clock to confirm Brennan’s new suspicion that Rockwell may not have been responsible for those crimes.
When a powerful member of the Iranian parliament kidnaps Arastoo (guest star Pej Vahdat) to have him aid in a murder case, Booth and Cam head to Iran, and the rest of the Jeffersonian team must race against the clock to help expose the killer. Meanwhile, Brennan discovers the truth about Booth’s growing gambling habit, and she turns to Aubrey for help to keep her and Christine safe from her husband’s menacing bookie.
When an affluent school teacher is found dead in an abandoned bookstore, the teachers and students at her school become suspects in the case. Meanwhile, Brennan’s publisher encourages her to join Twitter to help grow her fan base, and “squintern” Jessica Warren (guest star Laura Spencer) teaches Brennan some tricks to master the Twitter-verse, skills Brennan enthusiastically puts to use.
When the body of an ex-con is found in pieces, the Jeffersonian team investigates a local bakery known for employing former felons. But they soon learn that the victim was involved in a robbery gone bad, and start targeting suspects from the ex-con’s past. Meanwhile, “squintern” Arastoo Vazirir (guest star Pej Vahdat) must decide whether to return to Iran to visit his dying brother, which causes friction between him and Cam.
The Jeffersonian team unravels an unexpectedly competitive world of mini-golf as they try to figure out the murder of the sport’s superstar. Meanwhile, Brennan is worried her father Max is reverting to his criminal tendencies and “squintern” Wendell Bray enlists Hodgins to help him fix his girlfriend’s family heirloom
The investigation into who framed Booth for murder leads the Jeffersonian team to a conspiracy within the government that dates all the way back to J. Edgar Hoover. After additional DNA discovered on a previous victim is linked to the case, the team narrows down the list of suspects, leading them closer to cracking the case.
When the Jeffersonian team discovers the body of a renowned but disliked chess master amidst pig slop, Sweets surprises the team with his chess skills and goes undercover in the world of professional chess to find the killer. Cam is being recognized in the "Outstanding Woman of Science" issue of a noted science publication but is hesitant to participate since she does not want to offend Brennan who knows she should be the one to be honored. Meanwhile, much to Brennan's annoyance, Dr. Douglas Filmore, the always sunny Canadian forensic podiatrist fills in as a lab intern.
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. Meanwhile, Cam gets mistakenly arrested when her identity is stolen and Sweets decides to take a leave from the FBI.
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.
Pelant is back, and the members of the Jeffersonian team want to put an end to the hold he's had over them, once and for all. When a human cadaver is willed for research to the team, they devise a plan, with the help of Special Agent Hayes Flynn, to stage the human cadaver in a way that Pelant would stage a murder, and steal his spotlight in order to flush him out. But their plan backfires when Pelant is a step ahead of them, resulting in him killing someone close to Booth. Meanwhile, Sweets returns from his leave of absence and is convinced that Agent Flynn isn't the person whom everyone thinks he is.
The Jeffersonian team investigates the murder of Charlie McCord, a high school principal who, upon learning he had terminal cancer, created a website where people could go and pay for his inspirational videos. When the team finds a suspicious video of Charlie punching former UFC Light Heavyweight Champion Chuck Liddell in the face, it leads the team to Charlie's bucket list, which ultimately helps them get closer to solving the case. Meanwhile, Brennan and Booth finally start to plan their wedding and Sweets could be replaced by a virtual profiling system.
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.
While honeymooning in Buenos Aires, Brennan and Booth can't just relax on vacation. So, instead, they decide to help Raphael Valenza, a local detective and huge fan of Brennan's books, solve the murder of a Nazi war criminal whose remains were found in an historic mass grave. Meanwhile, back in Washington, D.C., Hodgins and Angela struggle to take care of Christine.
The Jeffersonian team investigates the murder of Sean Nolan, a failed model whose body is found intertwined in a beaver dam. The team soon discovers that Nolan's fruitless modeling career left his sperm donations as his only source of income. However, when the team learns that he falsified records, they start to suspect anyone who was jilted by his donations. Meanwhile, Brennan struggles with social niceties and tact when she is drawn into a feud with author Tess Brown and Hodgins gets in touch with his motherly instincts when he plays host to a fly larva.
Brennan is a juror on the case of professional soccer player Peter Kidman who is accused of murdering his wife. When she uses pure objectivity to help prove the killer not guilty, his best friend and a key witness in the case turns up dead. The Jeffersonian team must work together to prove that the soccer star was in fact guilty of killing both his wife and his friend.
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 Lana Brewster, a girl whose remains are delivered to Brennan and Booth's home by someone who believes her death 18 years ago was no accident. When the team discovers that Lana was murdered and her death was covered up, people from her past become key suspects, including an ex-boyfriend with whom Hodgins was friends. Meanwhile, Brennan starts having dreams again about evil tech genius Pelant, and about a potentially more heinous killer, whom she realizes could be involved with Lana's death.
The Jeffersonian team investigates the death of Brian Thomas, the head swim coach at a community college, whose remains were found dumped at the bottom of a well. When possible suspects tell Brennan and Sweets that Brian may have been having an affair, the team digs a little deeper only to find details of Brian's secret life. Meanwhile, Sweets fills in for Booth in the investigation while Booth prepares to testify before a Congressional sub-committee and the Jeffersonian team gets a new intern who catches Sweets' attention.
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 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.
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 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.
The remains of an escaped convict are found in a residential sewer, but an examination of the sewer pipes indicates that the murder occurred within prison walls. Brennan insists on solving the crime - despite Booth's pleas for her not to overexert herself - and the expectant couple experiences a very untraditional arrival of their baby daughter.
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.
Brennan and Booth head out to Los Angeles to consult on the production of "Bone of Contention," a film based on Brennan's latest book and the work of the Jeffersonian team. While on set, Brennan intervenes after finding flaws with the actors' performances, not to mention the film's total disregard for science. Then she discovers that the prop cadaver being used is an actual murder victim, forcing her and Booth to launch an investigation that has real-world consequences in the land of make-believe. Meanwhile, Booth is offered a job on the studio lot, and embarrassing information is revealed about Cam's past.
Evil tech genius Christopher Pelant, a suspect in a previous case Brennan and Booth handled, is back in court on appeal. Knowing what he is capable of, Brennan and Booth inform the judge that he is a suspect in two murder cases. Then, Brennan and Booth are called to the scene of a new murder. After determining the victim is Brennan's friend, who also is linked to Pelant, the Jeffersonian team works to prove he is guilty once and for all. But when law enforcement examines the team's findings, key pieces of evidence are tied to Brennan and suspicion falls on her.
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.
After an explosion occurs in a hotel garage, the Jeffersonian team must research the remains found at the crime scene in order to match them to the victim. The investigation only gets trickier when they discover that the man whom they thought was dead is actually alive. Meanwhile, Booth has to take on a desk assignment to get the department’s budget approved in order to land a promotion, so Sweets is given a temporary partner, FBI Special Agent Olivia Sparling.
The Jeffersonian team investigates the death of Jared Drew, an animal expo employee, and in the course of their investigation into his death, they enter the world of illegal animal trafficking. Meanwhile, Brennan thinks she would make an excellent presidential candidate, and Sweets and Daisy take on a big 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.
While investigating the remains of bodies that have been deemed unidentifiable, five “squinterns” uncover the identity of a man who died as a result of the 9/11 terrorist attacks, propelling the Jeffersonian team to determine if he was a perpetrator or a victim.
When a crime scene cleanup expert’s remains are found mysteriously sealed in an impenetrable pod that washed up on the beach, the team tackles one of their most challenging investigations. Meanwhile, Angela and Hodgins learn of a secret romance in which Cam is involved.
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.
The Jeffersonian team investigates the death of a young boy whose soul remains very much alive. When psychic Avalon Harmonia attempts to help the deceased's spirit cross over, each member of the team begins to question his or her own beliefs about 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.
Brennan and Booth investigate the death of a female roller derby skater whose body was dismembered. In order to get more answers, they enlist Angie to go undercover as a derby skater. Meanwhile, Cam tries to uncover the details behind Booth's secretive hospital appointments.
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.