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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. The businessman's body is found in a car on the train tracks, and at first glance, it is an apparent suicide. While investigating a possible connection between the two victims, Brennan and her team discover the businessman is still alive, but severely injured, at a local hospital, and the body at the scene is someone else. As the clues begin to unravel, the investigation gets more complicated when details of the man's private life are revealed, leading Brennan and Booth to a private detective who may hold key information. 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.

Booth and Brennan examine the remains of a woman and fetus found in the Delaware Bay. The body is identified as that of Carlie Richardson, a pregnant newlywed whose mysterious disappearance one year ago had been a major national news story. Carlie's husband Kyle Richardson is immediately thought to be the prime suspect in the case, but he disappears before Brennan and Booth can question him, prompting Booth to call for a manhunt for Kyle. Clues found with the remains throw suspicion in a different direction, and Brennan enlists Booth and her team at the Jeffersonian to recreate the potential scene of Carlie's murder to get a better idea of the build and body type of the murderer, with shocking results. Meanwhile, Booth is annoyed that his ex-girlfriend Rachel, the mother of his son Parker, is letting Parker spend so much time with her new boyfriend, forcing Booth to be more territorial than Rachel would like.

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. Brennan finds that his skull is cracked and his leg is broken, and Hodgins determines the victim has been in the trash heap for at least three weeks. At the lab, Angela is able to identify the body from a facial imprint created by the shroud. As Booth and Brennan try to unravel the limited clues of the case, the parents of the deceased boy point a suspicious finger at their son's young girlfriend, Kelly, a product of the foster system. Brennan takes her team members' rush to judgment and criticism of Kelly to heart since she's a product of the foster system as well. When Kelly confesses to the murder of her boyfriend, Brennan and Booth don't buy it, but are shocked and disheartened to discover who the real murderer is. Meanwhile, things get tense when Brennan and Cam butt heads over their different work styles and Brennan recoils at Cam's power plays. When a disagreement comes to a head, Cam threatens to start looking for Brennan's replacement, even if it means losing the whole Jeffersonian team if they're forced to take sides.

Moments after Booth and Brennan unearth the skeletal remains of a young girl, it becomes clear they aren't dealing with just any murder case. Hodgins, Zack and Cam confirm this back at the lab when they discover that the cause of death points straight to Howard Epps, a convicted serial killer who has been on death row for years; Brennan's previous testimony in his case gave Epps a stay of execution. Booth interrogates Epps, seemingly to no avail, but after finding a clue on the deceased girl that leads them to another young body - this one only a week old - they realize that Epps is forcing them to play a deadly game. 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. As precious seconds tick away, Brennan and her team must test their limits and confront their fears to save a young girl from becoming a victim.

After Booth has a bedroom romp with his ex-girlfriend Rebecca, he gets a call from Brennan about their latest case and agrees to meet her at a condominium construction site. They're led into a partially built unit where they find the gruesome remains of a man dissolving in a bathtub of household cleaning products. After determining the victim had Brittle Bone Disease, they search a database of area BBD victims, all of whom are children, and split up to visit them in hopes of finding a connection to the dead man. When both Brennan and Booth come back with confirmation 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.

Brennan and Booth are called to the site of an explosion in a Miami hotel where a young woman has been burned to death. Initially, the explosion is thought to be the work of a Colombian drug cartel intending to target Judge Dolores Ramos, the Colombian judicial representative. State Department official Alex Radziwill insists everything to do with Judge Ramos and the case go through him, which becomes both annoying and problematic when he stands in Brennan and Booth's way as they do their jobs in pursuit of key information about the case. When fingers point to Ramos' husband and son, Booth and Brennan are shocked to learn who was behind the murderous plot, and how far the State Department will go to protect a murder suspect.

Brennan and Booth investigate the death of Brianna Swanson, a young beauty queen whose decomposed remains are discovered at a Washington, DC, water filtration plant. Brianna's father is a suspect initially, but new clues lead Brennan and Booth to Brianna's dance school, where they glean key information. Meanwhile, Hodgins works up the nerve to ask Angela out on a date and after contemplating the pros and cons of dating a coworker, she agrees to go.

When the unearthed skeletal remains of Mason Roberts, a federal prosecutor who disappeared five years earlier, are discovered in the desert outside Las Vegas, Brennan and Booth suspect his death may be tied to the mob. The body count in the desert rises when vultures lead them to the recent remains of a young woman, just a few yards away. Booth suspects the same person may have been responsible for both deaths, but the woman's injuries lead Brennan to believe she has a long history of domestic abuse and her husband may have been responsible for her demise. Brennan and Booth question the deceased woman's husband, who denies he hurt his wife, but leads them to a Vegas loan shark. When an anonymous lead takes them into the world of gambling and underground ultimate fighting, Booth and Brennan go undercover as Vegas high-rollers. Booth takes his turn in the ring and risks his life in a desperate effort to uncover the mystery of The Woman in the Sand.

When the bodies of twin teenage boys kidnapped five years earlier are discovered in Pennsylvania, Booth and Brennan find themselves on the trail of the Grave Digger, a notorious serial killer whose M.O. is to kidnap, bury his victims alive and make a single, exorbitant ransom request. If the money is not paid in the specified period of time, there is no further communication and the victims are left to die. During the investigation, Brennan and her scientist colleague Dr. Hodgins become the Grave Digger's latest victims, forced to try to solve their own kidnapping from an underground grave.

When the headless body of a young man, along with a video camera full of documentary footage, is discovered in the DC-area woods, Brennan and Booth are called in to determine identify the year-old remains and determine if a murder was committed. The body is proven to be that of University of Virginia film student Graham Hastings, who had disappeared a year before while making a documentary about the local legend of a woman thought to be a witch who beheaded anyone who dared to look for her. In a mysteriously parallel set of circumstances, Brennan and the team find that Graham was beheaded by an axe. After examining the dark, chaotic and choppy footage from Graham's camera, Brennan and Booth learn that two other people - Graham's girlfriend Lori and fellow classmate Brian - were in the woods with Graham on the night of his disappearance. DNA on the axe used to murder Graham leads a shocking revelation of the killer�s identity. Meanwhile, Brennan befriends Graham's brother, Will, when she finds out that he, too, was an orphan, but the friendship quickly dissolves when the truth behind his brother's murder is uncovered.

When a man's body is found gutted, burned and hung up like a scarecrow on the roof of the Federal Building, Booth and Brennan are called in to identify the charred remains and determine who was behind the murder. Based on several factors, Booth determines the victim was a snitch working within an organized crime syndicate. Brennan's brother, Russ, tells her he got a mysterious call from their long-lost father, warning him they are in danger, and Brennan is contacted by a priest, who delivers a message from their father insisting she and Booth drop the case. Brennan and Booth determine the murdered victim was ex-FBI agent Garrett Delaney, who was tracking Russ and planning to kill him, giving more credence to their father's warning. As more clues come to light and a government conspiracy is revealed, Booth and Brennan make a shocking discovery as to who was behind Delaney's murder, and Booth is forced to make one of the most important decisions of his career, with very personal ramifications. Meanwhile, Zack must defend his dissertation, the last step to completing his doctorate, but needs some help from Angela to help him get taken seriously.

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', but that of a D.C. fireman Epps killed in order to fake his own death and escape from a maximum security prison amid the commotion of the fire. After paying a visit to Epps' former wife, Caroline, to determine if she has any clue as to his whereabouts, Brennan and Booth leave empty-handed, but are concerned for Caroline's safety with her ex-husband on the loose. Their fears are quickly realized as they get concrete proof that Epps has killed again. 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. While Cam conducts an autopsy on Epps' latest victim, Booth implores her to break protocol to save time and jump to a later step in the process. Against her better judgment she does, but she is sprayed with a deadly poison and critically injured. As Cam's life hangs in the balance, Booth, Brennan and the rest of the Jeffersonian team race to figure out what deadly substance is killing Cam and determine Epps' whereabouts before Cam becomes his latest victim.

After Booth maliciously shoots a clown ornament on an ice cream truck, his gun is taken away and he's forced to meet with an FBI psychiatrist to prove he's mentally stable in order to get his gun back. That leaves Brennan headed to Florida on her own to investigate the death of a young college student whose body is found inside that of a dead alligator. Since Booth is out of commission for the time being, her FBI counterpart on the case is Agent Tim Sullivan. Although he's easygoing, the two of them have communication problems and stylistic differences from the start and Brennan looks forward to when Booth will return to work. The alligator is shipped back to the Jeffersonian and the team determines the identity of the victim is young college student Judy Sloan, who disappeared several weeks before. As the Jeffersonian team works to unravel the circumstances surrounding the girl's death, Brennan finds she's more charmed by Sullivan than she cares to admit. Meanwhile, Booth has several meetings with FBI psychiatrist Dr. Gordon Wyatt, an Englishman with a unique approach to the situation who conducts their sessions in his backyard and assigns an unorthodox project to Booth, while surreptitiously getting him to talk about the potential reasons for his attack on the clown.

Brennan, Booth and the Jeffersonian team are called in by the Bancroft family, major donors to the Jeffersonian, to investigate the death of Terence Bancroft, who was found dead at home, bound to his desk chair and maliciously stabbed. The team proves the body had been there for almost a month. Booth questions Terence's wife, Clarissa, while the team brings the body and all the evidence back to the Jeffersonian for further tests. Hodgins removes an old photo of himself with the victim from official evidence so the others won't see it, knowing the photo links him to the case. When the case goes to trial and Hodgins' involvement is revealed, the Jeffersonian's reputation is jeopardized, prompting Brennan to make an important decision about her team. Psychiatrist Dr. Gordon Wyatt has cleared Booth to carry a gun and go back to work, but it's contingent on Booth continuing to meet with Wyatt on a few underlying issues - issues that may be creeping into Booth's judgment and affecting his investigative work. Meanwhile, Agent Sullivan invites Brennan to one of his basketball games and the heat is turned up on their relationship.

Brennan's latest murder-mystery is an immediate best-seller. Enjoying her success and her newfound love with Agent Sullivan, Brennan prepares to hit the publicity circuit to promote the novel. However, when she and Booth investigate a murder in the marina, they notice striking similarities between the case and one of the fictional murders in Brennan's book. A shaken Brennan grows impatient as her team suggests the murder was not an eerie coincidence, but the work of a copycat killer mimicking the murders in her novel. If this were true, the murder in the marina would be only the first of three gruesome killings, and the Jeffersonian buzzes with talk of what might happen next. Tensions build as Sully and Booth vie to protect Brennan and investigate possible suspects, including an overly obsessive fan who once stalked her. When a second murder is committed exactly like one of Brennan#s fictional killings, she is overwhelmed by the possibility of playing a role in the loss of innocent lives. With a potential third murder on the horizon, the team races to identify the copycat killer before the deadly final chapter unfolds:

Interrupting Brennan#s romantic vacation with Sully on his boat in the marina, Booth drags her to a crime scene on the river where the shell of a woman#s body is found minus all of her bones. The body poses an intriguing case for the team as they attempt to reconstruct the women#s skeletal structure without the help of any bones. Eager to get back to her vacation, Brennan quickly weighs in on the case, but in the absence of any bones, does not feel she has a reason to be involved. Zach, Hodgins and Cam attempt to construct a skeleton for the body, a task that proves to be both difficult and gruesome. During the process Cam finds the sole remaining bone in the deflated body, which is enough of a reason for Booth to barge back into Brennan and Sully#s vacation and bring Brennan into the Jeffersonian once again. Booth investigates an international mail-order bride agency as well as the woman#s former fiancÉ, but the man quickly evades the investigation. When further clues in the case point to a rare and ancient Asian custom that involves burying the bones of an unmarried woman with those of an unmarried man as a sort of afterlife wedding ceremony, Brennan and Booth realize they are in fact looking for a murder suspect who may have killed the woman found in the river to use her bones for the ceremony. Meanwhile, Sully propositions Brennan, forcing her to make an important decision about their future together, a proposition that surprises her and for which she#s definitely not prepared:

Water main bursts in the middle of the night at the historic St. Agatha#s church cemetery, leaving the cemetery grounds littered with coffins and their once-peaceful inhabitants, and Brennan is called in to identify and help re-inter the remains. Father Matt, a newly installed priest, has informed Brennan and Zack that the last burial in the cemetery took place over 50 years ago, but Brennan finds a skull buried less than five years ago, leading them to believe the body was buried to hide a murder. After meeting some opposition from cantankerous head priest Father Donlan, Brennan and Zack deem the once-consecrated ground a crime scene. They take the remains back to the Jeffersonian, where Booth is offended by Brennan#s lack of respect for his or anyone else#s religious beliefs, and the two struggle to find their rhythm, which has been disrupted ever since Sully left. Booth insists Brennan come with him to see his therapist, Dr. Wyatt, in hopes that Wyatt can help their relationship and get things back on track between them. Meanwhile, Hodgins and Angela#s romance heats up and Hodgins makes a bold move to advance things between them, taking Angela completely off-guard. When Booth and Angela return to the church to pass out sketches of the unidentified murder victim from the cemetery, a young parishioner identifies the sketch as the former parish priest Father Matt had replaced a short time ago. As Father Matt grows mysteriously ill and Brennan and Booth attempt to trace the details of the murdered priest#s disappearance, they must determine who is playing God and taking lives into his own hands:

Partial skeleton is found encased in cement, and Brennan, Booth and the Jeffersonian team are called in to investigate. Booth suspects the victim was killed by Hugh Kennedy, a member of a dangerous organized crime family. Complicating his plan to find and arrest Kennedy is the claim by a bounty hunter that she saw Kennedy burn to death in a car explosion, but the facts don't add up for Booth, and he tries to lure him out of hiding. But when Booth goes after Kennedy, the plan doesn't go as he envisioned and Kennedy kidnaps Booth, leaving Brennan to try to find Booth before he suffers the same fate as the original victim. Meanwhile, visiting her mother's grave, Brennan is paid a surprise visit by her father Max, who attempts to get her to listen to what he has to say about her deceased mother. Brennan is not willing to indulge her criminal father and does not hesitate to call the police, but Max is gone before they arrive. Max shows up again at her apartment, and still can't get her to listen to him before calling the police, but Brennan's reactions let Max knows he may be starting to get through to his daughter. After Booth disappears, Brennan turns to her father, who has extensive experience in avoiding the law, for help in finding Booth. As Booth's life and the life of his son are threatened for information he has on the case, Brennan and her father make an unlikely team who race to find Booth before it's too late.

Brennan and Booth rush to investigate a scene where a dead man has been found in a crater. It appears that the flattened body has fallen from a high altitude without a parachute, and when the remains are sent to the Jeffersonian for review, Hodgins' bone analysis leads him to believe that the body had been in outer space for a period of time. While Hodgins suggests multiple theories about extraterrestrial life and government conspiracies, Brennan and Booth attempt to discover the man's identity. They find out he was an astronaut named Colonel Howard who worked for the National Space Agency, and as they speak to his co-workers and family members, they struggle to extract pertinent information due to the confidentiality of his missions. When the team finds slash-like wounds on some of his bones, they discover that Colonel Howard's fall was no accident, and a complicated murder mystery unfolds. Meanwhile, thwarted in his previous attempt to propose to Angela, Hodgins tries a more traditional, romantic approach to winning her heart.

Brennan and Bones are called by Homeland Security to investigate the scene at an old stone house where some glowing bones have been found. Fearing the remains might be radioactive, the pair don protective Hazmat suits and cautiously enter the house, where they find the glowing bones but no radioactivity. Back at the Jeffersonian, the team examines the bones and determines the identity of the victim, but there is no immediate explanation as to why the remains are emitting a green glow. With each of their specialties called upon, the whole Jeffersonian team joins Brennan and Booth in pursuing the murder mystery, which leads them to a group of friends who are shocked to discover that one of their own is the victim. During the course of the investigation, the victim and their friends' MySpace.com pages, along with the photos, videos and blogs they contain, are a virtual tool for the Jeffersonian team's search for answers. Meanwhile, Hodgins professes his love for Angela in a very unusual .

The decomposed skeleton of what appears to be a young girl is found in a grocery cart in the D.C. area. Angela's reconstruction based on the evidence reveals the face of an 80-year-old woman, not a child, but the team learns the victim actually was a 22-year-old woman with a debilitating aging disease. Brennan and Booth's investigation leads them to the victim's mother, who points a finger at a former caretaker. But without a definitive lead, the team searches to find out who would want to take this defenseless woman's life, and the case strikes an especially emotional chord with Brennan. Meanwhile, Brennan's father, Max Keenan, reappears in Brennan's life in an attempt to make a connection with her and deliver information from her past, and she's surprised by her reaction. Hodgins and Angela walk down the aisle with Brennan and Booth as maid of honor and best man, respectively, but all does not go as planned.