Several questions were left hanging at the end of Season Two: What happened after Angela and Hodgins fled the altar, leaving Brennan and Booth to fill the gap? Will Zack go to Iraq? If so, what will happen to him there? Will Cam and Booth resume their on-again, off-again relationship? In the third season of BONES, Brennan and Booth find themselves on the trail of a serial killer who discards his victims' remains off freeway overpasses. Brennan also must deal with the trial of her father, Max Keenan, for the murder of the Deputy Director of the FBI.
In the third season premiere, a skull smashes through the windshield of some teenagers' car while they're driving on the freeway. While examining the skull, Brennan and Cam find marks on it made by human teeth, which implies cannibalism. Identifying the victim, Brennan and Booth go out to investigate, discovering a weird cannibalistic society as they try to solve the case. Meanwhile, Angela and Hodgins hire a private investigator to find her husband. Also, Zack returns to the Jeffersonian, and finds some crucial evidence to help solve the case.
Brennan and Booth investigate the death of a soccer mom who was blown up in her mini-van, confused as to why someone would murder a seemingly innocent soccer mom. They soon discover that the soccer mom, named June, was part of a group of radicals from the 70's, named the National Liberation Army. June was also wanted by the FBI for decades, and might have been close to turning herself in, which makes motives for her murder really complicated. Meanwhile, Brennan goes to see her father Max in jail.
The team investigates a decomposed body that was discovered in the woods with bound arms and missing feet. Things get kinky when Booth and Brennan are led to a lodge that's 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.
Booth and Brennan examine a severely decomposed body found by some teenagers on hospital grounds. They identify the body as a man named Franklin Curtis, who was the founder of an organic supermarket chain, and discover that the body was either cooked or incinerated. Booth and Brennan go out to question people around Curtis' farm, while back at the lab it is discovered that the flesh of another victim was with Curtis'. Meanwhile, Booth and Brennan are assigned to a psychologist.
A Halloween pumpkin patch maze becomes a lot scarier when the mummified remains of a young girl are found in it. Booth and Brennan go to investigate, and are shocked to find that the victim has been dead for over a year. To make the situation even creepier, a second body is found at a Halloween amusement park funhouse, again mummified, but this time dead for approximately two years. Booth and Brennan get wind of a third missing girl and link her to the person who killed the other two girls. They must now race to find the killer before he or she strikes again this Halloween.
The team suspects their own colleagues after the burnt remains of an intern at the Jeffersonian are found in the building's incinerator. At first it's thought that she might have been killed because she was working on an artifact in the Widow's Son case, but then things become more complicated when romantic ties between her and another employee at the Jeffersonian surface. Meanwhile Booth poses as Cam's boyfriend on one of her family get-togethers.
A high school time capsule from 1987 is opened – and contains a teenager's liquefied remains; only the skeleton is intact. Gil Bates, former high school nerd and current assistant manager at Tech Town, tells Booth and Brennan that he sealed the capsule himself, and he doesn't know how the body got in there.
Booth has Cam rather than Brennan accompany him to a crime scene, where a stabbed, kneecapped, naked corpse is found. There's a jade gemstone inside the stab wound. At the lab, it's found that the kneecaps were surgically removed.
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 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.
A body is discovered at Homestead Natural Hot Springs in a spring filled with mud. Booth and Brennan go to investigate the scene and find that the body is that of Tripp Goddard, a sexy motorcycle racer who had been murdered about two weeks ago after a race. Sweets' girlfriend is also introduced.
A wannabe singer Tommy Sour is found in a grassy location. The investigation leads Brennan, Booth, and Cam to the restaurant where Tommy used to sing and where several suspects who took part in the open mike contest are, including a woman who was obsessed with Tommy and turns her affections towards Booth after learning of Tommy's death. Also, something horrible happens during the investigation which shocks the Jeffersonian team.
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.
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.
Booth lies dying as Brennan tends to him. The image fades from Brennan's memory and she's back in the lab, working on a skeleton. The squints file in, dressed in black, ready to attend Booth's funeral. Brennan tells the solemn group she won't be attending. She doesn't see the significance in gathering around a hole in the ground. Angela pulls Brennan aside. She needs Brennan, her best friend, to be at Booth's funeral with her if she's going to get through this tough time. Brennan agrees to go, for Angela.