Booth and Brennan head across the pond to the UK where Brennan guest lectures at Oxford while Booth speaks at Scotland Yard. While there, local officials ask for their help on a high-profile murder case involving a British heiress.

While in London, Booth and Brennan aid in a murder investigation where they team up with Dr. Ian Wexler and Inspector Cate Pritchard. Back in D.C., the Jeffersonian team leads their help in the case, but is surprised when Angela's long-estranged husband returns.

After a decomposed body of the host of a popular reality show is found in an outhouse, Booth and Brennan must track down the killer out of a large group of suspects, most of which were humiliated on the victim's TV show. Meanwhile, Booth tries to comprehend Brennan's romantic life after he finds out she is involved in two relationships.

When Parker finds a severed finger in a bird's nest while playing with Booth, the team gets together to find the rest of the body. After the body is found in Jefferson Memorial Park, it is revealed that the death was a murder. With the help of a new grad student, the team is able to identify the body as a local veterinarian with a gambling problem. This fact leads them to an illegal dog fighting ring where, with the help of Cesar Millan, the team is able to gather enough evidence to track down the killer.

When a teenager comes across a dismembered body in a pool of purple water, Brennan and Booth are called to the scene. There they find that the victim's head is missing. With help from the newest grad student, Wendell, the team learns the body is that of Jared Addison, a 25-year-old science fiction writer with severe OCD. Sweets lends his expertise to the case as Booth and Brennan interview suspects, which includes Jared's psychologist. Meanwhile, a person from the group's past gives them insight into the case.

When the remains of a manager are found in an office building's elevator shaft, Booth and Brennan must attempt to find which employee had the most motive to kill their boss. Meanwhile, Brennan's latest grad student, who has a very bleak and morbid outlook on life, lends his insight.

When skeletal remains are found in the Chesapeake Bay, Brennan and Booth are on the case to investigate. With only the upper torso of the victim intact, the team has little to work from besides the remnants of the victim’s breast implants. Brennan and Booth are led to a small church community in Maryland where the victim was a pastor, but they have no record of her existence prior to moving to the small town five years prior. When the victim’s lower half is discovered, the team realizes their initial assumptions about the victim may not be correct. As Sweets lends insight to the victim’s psychological state and Brennan’s latest grad student adds his own offbeat observations, the team must decipher who would have wanted her dead. From possible love interests to her family to the parishioners at the church where she was a pastor, the anatomy of the case is very misleading.

An impounded junkyard car contains the crushed remains of a famous artist, leaving Booth and Brennan to determine if there was foul play or not. The suspects range from his rivals to his own assistant, causing the team to race the clock and find evidence of a murder before the smashed vehicle must be relinquished to put on exhibit for an art show showing an artists self sacrifice for his art. Meanwhile, Roxie, the ex-girlfriend of Angela, becomes a prime suspect due to her work with the artist. So Angela and the team must work to find who delivered the final artful stroke to the artist.

Booth's brother, Jared, and Brennan investigate after a body is found uring a police raid. The team learns the victim is an inventor's father who had a difficult past with his son. But when a second body is found, the team must race to find the con man in the inventor's life. Meanwhile, Brennan goes on a date with Booth's brother and learns a lot about Booth's past.

Booth and Brennan travel to China to help identify pre-historic remains, but while on the flight, a human body is found in the plane. In order to solve the crime, Booth and Bones must get equipment from the passengers in order to piece together a devise to send evidence back to The Jeffersonian before they lose jurisdiction. Back in the U.S., Hodgins begins to move on after his break-up with Angela, while Angela and Roxie grow closer.

Brennan and Booth investigate when several skeletal remains are found on protected grounds. The team uncovers that the remains are that of an ex-Marine who has been AWOL for 3 years. Clues leads Booth and Brennan to an elite private school where the ex-Marine had worked as a manny for one of the rich families.

Booth and Brennan investigate the remains of conjoined twins found in a shallow grave in a remote desert area on the Texas-Oklahoma border. Back at the lab, the team determines the skeletal remains to be those of Jenny and Julie, who were jugglers in a traveling circus. Knowing there is no way the circus folk will talk to anyone outside their tight-knit clan, Brennan and Booth must infiltrate the circus community in order to find out more information about the twins, ' deaths. Honing Booth, 's Ranger knife-throwing skills, the duo goes undercover as knife-throwing act Buck and Wanda Moosejaw. As they encounter a variety of suspects among the colorful circus crowd, including ringmaster Henry Simon, a rather raucous clan of clowns and a tempestuous strong man who may have been romantically involved with one of the twins, Booth and Brennan find the circus experience to be quite the spectacle.

After a volunteer fireman is found dead at an ice rink, Booth and Brennan are called to investigate. However, when information surfaces that Booth may have a conflict of interest in the case, he is removed from the investigation and becomes a suspect himself.

Booth is kidnapped by the Grave Digger and the Jeffersonian team must find and save him before it’s too late. Meanwhile, when evidence from the Grave Digger’s case goes missing, Brennan and Hodgins are suspected of taking it.

Bones and the team are called to investigate when a woman is murdered during a sci-fi convention. While Booth is out with an injured back, Agent Payton Perotta arrives to help with the investigation.

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.

Booth and Brennan are called when a human body is found buried in a mound of salt onboard a de-icing truck. They find the victim was a pregnant 16-year-old high school student and soon learn that half of her teammates on the school volleyball team were part of a secret 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. There they learn the victim had been a part of a controversial project, Brennan and Booth must investigate the several death threats she had received. Meanwhile, Angela's father arrives in town to confront Hodgins.

Booth and Brennan are called when an image of the Virgin Mary is found in a bale of compressed cardboard. They find that the image is in fact a bloody outline of a body that has been flattened inside of the cardboard bale. Once the victim is identified, Booth and Brennan retrace her final moments and find the vicitim was involved in shady relationships. Meanwhile, Booth and Brennan become suspicious when they see Daisy, Sweets’ girlfriend, trying on wedding dresses with another man; and Hodgins and Angela come to terms with their relationship.

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 vicitim was an American citizen. The team links the skeleton to a U.S. death metal band and Booth and Brennan must venture into the death metal music scene in search of the killer. Meanwhile, Sweets goes to Dr. Gordon Wyatt for input on a book he's writing about Booth and Brennan, and Dr. Wyatt gives him a new perspective on the duo's relationship.

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. Brennan then convinces Booth to help her steal the body, leading them into a bizarre mystery surrounding the actual cause of death. Meanwhile, Cam gets a crash-course in parenting when she must convince her newly adopted daughter to quit smoking.

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 and soon find a canal in which they discover Sachi's decapitated head. Ken arrives in Washington and Booth and Brennan work with him to retrace his sister's final moments to find her killer.

A frat boy is found dead inside a college mascot uniform, Booth offers to help his brother Jared find a new job.

After a body of a wine critic was found inside a barrel of wine the team investigate that the wine critic gave a bad review which lead to the closure of the vinyard.Everybody from the wife to the owner are a suspect. Meanwhile, Booth finds out he has an undiagnosed health problem and to add to that Brennan tells him she wants a baby, his. That dredges up all kinds of unspoken feelings and unresolved issues between them. The stress is to much for Booth and he is visited by Stewie Griffin (Family Guy) to lend his advice in his own inimitable way to Booth.

In the Fourth season finale a body is found murdered at The Lab, a popular nightclub, and everyone is a suspect. In an unusual twist of storytelling, Brennan, Booth and the Jeffersonian team take on various roles outside their normal duties, including serving as the nightclub staff as well as local law enforcement.