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| Brennan and Booth investigate the site of a train wreck where the bodies of a senator and a high-profile businessman are found within the wreckage. Meanwhile, Brennan is introduced to Dr. Camille Saroyan, a first-rate pathologist who has been hired as the head of forensics at the Jeffersonian, and more importantly, Brennan's boss. It doesn't take long for Brennan to figure out "Cam" is a little too familiar with Booth and that they share something of a past. Also, Booth encourages Brennan to visit her mother's gravesite for the first time
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| Booth and Brennan investigate the remains of a woman and fetus washed up on the beach of the Delaware Bay. The body is identified as that of Carlie Richardson, a pregnant newly-wed whose mysterious disappearance one year ago had been a major national news story. However, the immediate prime suspect, Richardson's husband, has also disappeared. Meanwhile, Booth is annoyed that his ex-girlfriend Rebecca, the mother of his son Parker, is letting Parker spend so much time with her new boyfriend.
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| Brennan and her team dig though the trash to find clues when a young man wrapped in a shroud is found among garbage. After Angela is able to identify the deceased boy, Cam quickly assumes the main suspect to be the boy's girlfriend, Kelly, who is a product of the foster system. Brennan is hurt by this as she is also a product of the foster system. Meanwhile, things get tense when Brennan and Cam struggle for power in their disagreement on work styles. Cam threatens to fire Brennan even if it costs her the whole Jeffersonian team.
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| Skeletal remains of a young girl are found, and when brought back to the lab, the team recognizes this is not just any murder but that of Howard Epps, who the team encountered in the first season, a convicted serial killer on death row. He left clues leading to another body, a fresh kill that is only a week old. Brennan and her team scramble to decipher Epps' cryptic clues as they try in a desperate effort to find his accomplice who has been killing for Epps. When they realize that another victim may be alive, the team works under pressure to try to find the young girl.
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| Gruesome remains of a man dissolving in a bathtub of corrosive chemicals are found in a construction site. In a search of the man's identity, they realize he was living a double life with two different families. In what first appears to be a straightforward case of jealousy and insurance money, new clues send Brennan and Booth in a completely different direction and a third suspect is brought to light. Meanwhile, Brennan, curious, confronts Rebecca about her recent antics with Booth and her rejection of Booth's marriage proposal.
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| Brennan and Booth are called to the site of an explosion in a Miami hotel where several people were either injured or died, including an unidentified body that was found burned, thought to be that of the bomber. Initially, the explosion is thought to be the work of a Colombian drug cartel intending to target Judge Dolores Ramos, the Colombian judicial representative, who survived the blast. Diplomatic immunity and State Department official Alex Radziwill stand in way of Brennan and Booth's investigation as they pursue key clues about the case.
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| Brennan and Booth investigate the death of Brianna Swanson, a young beauty queen whose decomposed remains are discovered at a water filtration plant. Brianna's father is the initial suspect, but new clues lead elsewhere. Brennan and Booth investigate Brianna's dance school, where they find new information leading to several suspects. Meanwhile, Hodgins works up the nerve to ask Angela out on a date. At first, she rejects due to their situation as co-workers but after seeking advice from Brennan and Cam, she agrees to go.
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| The team investigate the murder of a missing federal prosecutor and a related murder of a female boxer. Booth and Bones go undercover to infiltrate an underground fight circuit in Las Vegas.
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| The team investigate the murder of two kidnapped teenage twin boys. The boys were placed in a spaceship-like capsule and buried alive underground. Soon, Brennan and Hodgins find themselves victims of the "Grave Digger", and Booth frantically searches for them as they slowly run out of oxygen underground. The case as broadcast has no conclusion (it will be solved in season 4). The Fox Network website initially displayed a summary for the episode which included an original ending where the Grave Digger was identified as the female reporter that coauthored a book about Grave Digger.
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| Brennan and Booth investigate the death of a young Blair Witch style film-maker.
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| Zack defends his dissertation to obtain his doctorate and asks help from a colleague. Meanwhile, 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 hotel that housed Federal witnesses. Booth determines the victim was a snitch working in an organized crime syndicate. Brennan's brother, Russ, informs her of a phone call he received from their father, warning him that they are both in danger. Soon after, a priest contacts Brennan telling her that her father insists that she and Booth drop their case. They determine that the body found was actually an ex-FBI agent, who was tracking Russ to kill him - hence, giving reason to Brennan's father's warnings.
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| Booth and Brennan are ordered to the cell of serial killer Howard Epps to identify the remains of an inmate. To their surprise, the charred remains don't belong to Epps. It's soon learned that Epps has escaped and is on a revenge path, which involves Booth's young son, Parker. Due to the danger of the case, Brennan must get FBI protection. Cam inhales a toxin while performing an autopsy, which puts her life in danger.
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| When Booth is ordered to go see a psychiatrist after irrationally discharging his firearm, Brennan is paired up with Agent Tim Sullivan to investigate the apparent murder of a college student in the Everglades, and by the time the case is solved Sullivan and Brennan express their mutual interest in each other.
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| When a benefactor of the Jeffersonian is found murdered, it's up to the team to find out who, but Hodgins' past with the widow complicates matters. Meanwhile Booth continues to see the therapist, and Brennan is progressing in her exploratory relationship with Sullivan.
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| Three separate bodies are found murdered exactly the way Brennan wrote them in her new book. However, the killer's method was different every time, leading the team to believe that it was not one but three killers. Booth and Sully become concerned for Brennan, while she insists she can take care of herself. This increases tension between Sully and Brennan, straining their relationship. Booth tries to help them along, apparently fine with the couple. At the end of the episode, Sully and Brennan reconcile and Booth, walking away, looks back sadly.
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| During Brennan's vacation, a woman's body is found with its bones removed. The team interviews people who knew the woman, but they all seemed to be hiding something. Meanwhile Sully tells Brennan that he had bought a boat and will be leaving for a year, at the end of the case, to give tours of the Caribbean. At the end of the episode Sully sails off in his new boat, "Temperance", while Brennan waves good-bye.
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| Brennan and Zack examine corpses, which have been spilled out of their coffins, due to a burst water main in an old cemetery on the St. Agatha church grounds. However, as they identify the individual bodies to be put back in their proper place, they find one skeleton that is out of place. Father Donlan, who runs the church, says that all these bodies had been buried for at least 50 years and yet Brennan believes one of them was buried five years ago with no coffin. When it is confirmed that the deceased was murdered, Booth and Brennan investigate the priests and administrator of the church and argue about the validity of religion.
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| The remains of a body are discovered encased in concrete, and Booth has a hunch the victim is connected to an organized-crime boss. Meanwhile, Brennan's estranged father pays her a visit.
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| The team investigates the death of an astronaut who appears to have fallen to Earth from a high altitude. While Brennan and Booth question his associates at NASA, Hodgins theorizes about a conspiracy involving extraterrestrials.
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| A glowing skeleton is found at an old stone house, and Brennan and Booth are called to investigate. After being checked for radioactivity (and discovering none), the bones are sent to the Jeffersonian where the team identifies the victim and learn that the blue glow is caused by a fluorescent bacteria from sea urchins that entered her bloodstream. The whole team gets involved as each of their specialties is needed. Their investigation leads them to a group of friends who own a restaurant and are shocked to learn that one of them is the victim. The Jeffersonian team uses the victim's MySpace page, along with the blogs, videos and photos to search for answers. Meanwhile, Hodgins shows his love for Angela in a very unusual way.
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| The team works on finding how Chelsea Cole, a fan of astronomy who suffered from Werner's Syndrome, died. Meanwhile, Hodgins and Angela prepare for their wedding. Zack is asked to serve his country in Iraq. Brennan's father, Max, tries to let her in on her past and brings her a 1993 video of her mother. Booth and Max decide to get into a fist fight before Max surrenders to his arrest.
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