Episode 1: The Titan on the Tracks

Brennan and Booth investigate a train wreckage where the bodies of a senator and a high-profile businessman are found. The businessman's body is found in a car on the tracks, initially suggesting suicide - but clues begin to unravel which complicate the case. Brennan also has to deal with the arrival of the new head of forensics at the Jeffersonian, first-rate pathologist Dr. Camille Saroyan.

Episode 2: The Mother and Child in the Bay

Booth and Brennan examine the remains of a woman and foetus in Delaware Bay. The body is identified as Carlie Richardson, a pregnant newlywed whose mysterious disappearance one year ago had been a major national news story. Booth calls for a manhunt when Carlie's husband Kyle - the prime suspect - disappears. Clues found with the remains throw suspicion in a different direction, and Brennan enlists Booth and the team to recreate the potential scene of Carlie's murder to get a better idea of the build and body type of the murderer. Meanwhile, Booth becomes territorial when his ex-girlfriend Rachel is lets Parker spend so much time with her new boyfriend.

Episode 3: The Boy in the Shroud

Brennan and Hodgins join Booth and Cam at a crime scene beside an overturned garbage truck. Among the trash in the truck is the body of a young man wrapped in a shroud. As Booth and Brennan try to unravel the limited clues of the case, things get tense between Brennan and Cam who threatens to start looking for Brennan's replacement, even if it means losing the whole Jeffersonian team.

Episode 4: The Blonde in the Game

When a young girl is murdered, the evidence points to Howard Epps a convicted serial killer who has been on death row for years. As the body count rises, Brennan and her team scramble to decipher Epps' cryptic clues in a desperate effort to find his cold-blooded accomplice. The team is pushed even further when it is revealed that the latest victim may still be alive, with only hours left to live and the team must try to stop the killer before another young girl becomes a victim.

Episode 5: The Truth in the Lye

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.

Episode 6: The Girl in Suite 2103

Booth and Brennan are on the case when an explosion at a Miami hotel kills a young girl, and are forced to fight the US government to bring the murderer to justice.

Episode 7: The Girl with the Curl

The remains of 10-year-old beauty queen are found at a water filtration plant, leading Booth and Brennan to explore the world of beauty pageants.

Episode 8: The Woman in the Sand

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. They then find the body of a woman a few yards away, who they suspect was killed by the same person. The woman's injuries lead Brennan to believe she had a long history of domestic violence. When the husband denies having hurt his wife, they are led to a Vegas loan shark, where an anonymous lead takes them to the world of gambling and underground ultimate fighting, where Booth and Brennan go undercover as Vegas high-rollers. In an attempt to uncover the mystery, Booth risks his life.

Episode 9: The Aliens in a Space Ship

The bodies of twin teenage boys, kidnapped five years earlier, are discovered. Booth and Brennan follow the trail of a notorious serial killer, known as the Grave Digger. His M.O. is to kidnap, bury his victims and ask for a ransom. If the ransom isn't followed, the victims are left to die. During the investigation, Brennan and a fellow colleague become the latest victims. Both are forced to solve their own kidnapping from an underground grave.

Episode 10: The Headless Witch in the Woods

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 talk about mixing work and personal lives.

Episode 11: Judas on a Pole

Booth and Brennan are called to the scene where a man's body was found gutted, burned and hung like a scarecrow on the roof of a Federal Building. Brennan's brother, Russ, informs her of a phone call he received from their father, warning him that they are both in danger.The deeper they get into their case the more the learn, and finally make a shocking discovery that can cause serious repercussions for Booth and his career. Meanwhile, Zack must defend his dissertation to obtain his doctorate, asking help from a fellow colleague.

Episode 12: The Man in the Cell

Brennan and Booth are called to the scene of a deadly fire at a D.C. prison to investigate what they believe is the death of Brennan’s incarcerated adversary, serial killer Howard Epps, whose body was found burned beyond recognition. But Brennan’s examination leads to the chilling realization that the charred body is not Epps’ who has faked his own death and escaped from a maximum security prison amid the commotion of the fire. As Epps leads Brennan and Booth into a game of cat and mouse, it’s clear he is targeting them and the people they’re close to, all the while giving them clues they desperately try to decipher before Epps takes another victim.

Episode 13: The Girl in the Gator

Brennan has to work with another agent while Booth needs to see a therapist (played by Stephen Fry). The duo investigate the death of a college freshman, who took part in a 'Girls Gone Wild' type of video.

Episode 14: The Man in the Mansion

Booth and Brennan investigate the death of Terence Bancroft, one of the Jeffersonian's major donors, found dead at home. Hodgins' compromises the case and the reputation of the lab when he removes some evidence that would link him to the Bancroft family and to the case itself. Due to this, Brennan must make an important decision about her team. Meanwhile, Booth, although cleared by Dr. Wyatt (guest star Stephen Fry) to use his gun, must continue to meet with the psychiatrist and Agent Sullivan invites Brennan out.

Episode 15: The Bodies in the Book

Brennan and Booth have to solve two cases, both highly similar to those in Brennan's new book on the bestsellers list.

Episode 16: The Boneless Bride in the River

The team investigates the death of a Asian woman without any bones left in her body. Sully proposes something to Brennan that she does not expect.

Episode 17: The Priest in the Churchyard

A water main bursts in the middle of a cemetery, leaving lots of coffins to litter the grounds. Brennan is called in to identify the remains so they can be reburied. When she finds the remains that have only been there for five years after being told no one was buried their in fifty years. Booth decides to bring Brennan to see his shrink so that they can work on getting their relationship back on track. Things get intense between Hodgins and Angela, when Hodgins makes a bold move.

Episode 18: The Killer in the Concrete

Booth and Brennan investigate the case of a partial skeleton found in cement. Booth thinks a member of a crime family - Hugh Kennedy - is to blame, but when he hears word that Hugh was burnt to death in a car things get more complicated. Booth finds out that Hugh is actually alive, but then gets kidnapped by him. Brennan must now find Booth before he is hurt, but this is harder to do than she thinks, and she ends up going to great lengths to get Booth back safely.

Episode 19: Player Under Pressure

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, Kamaria Manning, and George Francis, who acted as a sort of advisor for the deceased. The team start questioning Francis and a lot of people about the athlete maybe using drugs. Angela and Hodgins have an important talk. Zack is overwhelmed by having to reconstruct the crushed bones to form a skeleton.

Episode 20: Spaceman in a Crater

A mysterious dead man is found in a crater with his body flattened as if he had fallen from the sky. Brennan and Booth try to find out who the man was while Hodgins comes up with different conspiracy theories involving aliens. Booth and Brennan find out the man was an astronaut who was murdered, and a complicated murder case unfolds.

Episode 21: Glowing Bones In A Cove

Glowing bones are found in an old stone house, and Brennan and Booth are called in to investigate. They find that strangely, the bones are not radioactive and lack any other explanation for why they would be glowing. With the victim identified, the team sets off to figure out the murder mystery.

Episode 22: Stargazer In A Puddle

The decomposed skeleton of a young woman is found in a shopping cart, but due to an aging disease she is reconstructed by Angela as an 80-year-old woman. Booth and Brennan investigate and are led to a former caretaker of the victim, but their lead is shaky and they have trouble finding out who would want to kill such an innocent young woman. Meanwhile, Max Keenan, Brennan's father, reappears with information from her past. Also, Hodgins and Angela walk down the aisle, but everything doesn't go as planned.