Seven months have passed since the end of season 5 and Caroline Julian calls the team back to the Jeffersonian in Washington, D.C. to help save Cam’s career as they work to help solve a controversial case regarding the remains of a young boy. The team work on trying to discover the identities of a couple whose bodies were found in a cave. Booth’s war correspondent, Hannah Burley, returns to Washington, D.C. and Brennan re-evaluates her relationship with Booth after realizing he’s genuinely happy with Hannah. Booth and Brennan investigate the remains of Richie “The V” Genaro, who was last seen partying in a Jersey Shore nightclub. Brennan’s pop culture knowledge is tested when she believes she watched a documentary about the people in Jersey Shore, but was actually a reality show. Meanwhile, Hannah makes friends with the Jeffersonian team and Angela tries to keep her pregnancy a secret. The team goes on a search for missing body parts after they find a decomposing skull and hands in a dumpster. After the victim is identified as a bounty hunter who was searching for a killer named Charles Braverman, the team discovers that someone else is looking for Braverman as well, resulting in a chase with an unexpected suspect. Meanwhile, Brennan makes children’s show star Professor Bunsen Jude “The Science Dude” her new intern.
A ballet dancer is murdered and Booth and Brennan are led to suspect a group of street dancers in the crime. Meanwhile, Booth’s girlfriend Hannah is shot, leaving Booth to worry about her health. The team tries to identify the months old remains of a young man found in a 150-year-old slave ship while identifying the slaves from the ship’s last voyage. The investigation leads Booth and Brennan to a cruise which caters to older women looking for younger men. Meanwhile, Sweets has trouble keeping a platonic relationship with Daisy and Cam finds a personal connection to the slave ship. When human remains are found in the world’s largest chocolate bar, an eccentric candy mogul falls under suspicion. The team investigate the puzzling way the remains got there. Meanwhile, Cam is worried about what college Michelle attends and Hodgins plans a party to reveal Angela’s pregnancy, even though everybody already knows. A burnt corpse found in a truck leads Brennan and Booth to a local high school where the victim’s wife works, and they find evidence of an illicit relationship between a teacher and a student. Meanwhile, Hannah tries to form a bond with Booth’s son and Sweets helps Daisy with a government psychological exam.
Brennan discovers the body of a surgeon found in a tough neighborhood with multiple skull fractures, but no indication of why or how she was there. Brennan begins to identify with the victim after learning more about her past. The case leads Brennan to retrace the final steps of the victim’s life to help solve the case. She also makes a discovery about herself and learns a lesson about taking chances with the help of a Jeffersonian security guard, Micah Leggat (Enrico Colantoni). Hannah discovers Brennan and Booth’s past and starts avoiding Brennan, pushing Brennan to confront her. A case involving a liquid explosion of human remains causes Brennan, Booth, and Cam to become covered in evidence. Sweets believes Booth still has feelings for Brennan. Hodgins and Angela begin to talk about their future including where they want to raise their family. Heather Taffet aka “The Gravedigger” (Deirdre Lovejoy) faces her final appeal before being sentenced to death. When she is killed by a professional sniper, the team investigates the identity of the shooter, leaving both Booth and Brennan’s father, Max as possible suspects. Sweets deals with the aftermath of the shooting as he was very close by when she was killed, and also what Taffet said to him earlier about being a “weak link”. Booth eventually discovers the shooter is Jacob Broadsky (Arnold Vosloo), a professional sniper and mentor that he once knew. Booth and Brennan investigate the death of a man who was found in a cornfield. The man was a polygamist, who was married to three women, who are also sisters. Cam believes her relationship with her boyfriend is in trouble, so they try and make it a priority.
The remains of a BMX rider are found on the roof of a warehouse after a failed stunt attempt. The team investigate the accident and determine he was killed by blunt physical force, indicating he was murdered. Sweets asks Booth for advice as he plans on proposing to Daisy, while Booth proposes to Hannah showcasing his commitment. Hannah declines, saying she can’t commit. On Valentine’s Day, the team investigate the liquefied remains of a wedding planner found in her home. Cam pressures the team to solve the case so she can spend time with her boyfriend to celebrate the holiday. Booth and Brennan both downplay the significance of Valentine’s Day, while Hodgins plans a special day for Angela. After successfully killing the Gravedigger, sniper Jacob Broadsky strikes again, killing a prior suspect who escaped the justice system. Booth uses his military training to try to stop Broadsky before he hits another intended target. Angela’s father (Billy Gibbons) visits the Jeffersonian where he insists on being able to name his unborn grandchild. A blizzard that causes a citywide blackout, the team must think of creative ways to solve a murder case that could be connected to a possible viral outbreak of Crimean–Congo hemorrhagic fever(CCHF). Booth and Brennan are trapped inside the elevator in Booth’s apartment during the blackout, with Sweets outside where he starts a touchy conversation concerning their relationship. Meanwhile, Angela and Hodgins receive troubling news that could affect their unborn child. After a flood on the U.S.-Canada border, eight pairs of dismembered feet are discovered, with seven pairs being identified as research corpses from a nearby university body farm. Brennan forms an alliance with Canadian forensic podiatrist Dr. Douglas Filmore when he takes the remains to Canada. Meanwhile, Cam continues to make college plans for her daughter, which her daughter may not like. The remains of a host of a mythbuster television show are found in the wilderness and appear as he was killed by the mythic reptile-mammal hybrid known as the Chupacabra. The victim was attempting to debunk the myth. Meanwhile, Jeffersonian intern Vincent Nigel-Murray, who is a recovering alcoholic, makes amends as well as confessions to the team.
The remains of a maritime museum security guard are found in the Florida Everglades, after attempting to steal an 18th-century nautical chart fragment that is used to discover treasures. To help solve the crime, Booth gets the help of Walter Sherman (Geoff Stults), a former U.S. soldier and Iraq war veteran, who has the ability to unearth anything. Along with Sherman, they are also assisted by his colleagues, Ike Latulippe (Saffron Burrows) and Leo Knox (Michael Clarke Duncan). During the case, Brennan tests Sherman’s skills, while Booth has cold feelings about his former military comrade. The team investigates a murder of an ad man whose remains were found on a community center playground. After investigating, they learn the victim burned bridges by having an aggressive attitude and by being brutally honest. Meanwhile, the team tries to be more honest in their relationships, and Angela has Hodgins face the reality of their pregnancy. The team believes a 15-year old Jane Doe, who is deaf and refuses to communicate, potentially committed murder. She was found covered in blood and holding a knife. Meanwhile, Hodgins is unaware of details regarding their pregnancy, because Angela has kept details from him. Bones struggles with her inability to convey emotion.
Booth and the Jeffersonian institute continue to search for Jacob Broadsky, and his more recent phone call to Booth suggests he intends to go after his team. Booth finds another body in a piece of land Broadsky was believed to be in, a former fellow sniper; Broadsky has taken his rifle. While examining the body, Broadsky kills Vincent Nigel Murray, though the intended target was Booth. While the rest of the team struggles with their colleague’s death, Booth becomes more determined to catch Broadsky once and for all. Brennan spends the night in Booth’s apartment, and while conversing with Montenegro it is implied she slept with him. Hodgins learns the bullet used to kill Murray came from a port, and that Broadsky’s right hand is broken from killing his friend. At the showdown, Booth shoots Broadsky in the leg, and he is arrested. In the end the team honor Murray by singing his favorite song, “Coconut” while taking his body to be sent to England. Some unidentifiable and gruesome remains were lodged in the pinsetter at a bowling lane and evidence suggests foul play. Booth and Brennan go undercover in a bowling league with the help of Brennan’s father Max, who used to be in the victim’s bowling team. Meanwhile, Angela works from the hospital via webcam as she comes closer to giving birth. The episode ends with Brennan telling Booth that she is pregnant and that he’s the father of her unborn child.
This season is really memorable due to – the death of the Gravedigger, Angela & Hodings getting pregnant and having a son, the sad death of Vincent Nigel-Murray (and his friends/colleagues singing his favourite song as they bid him farewell), the intense Broadsky and his trying to kill Booth ending up with Vincent’s death and ofcourse after heartbreak due to Booth finding a steady girlfriend and then later Booth & Brennan finally getting together and Bones getting pregnant! I rate this the best & most emotional season yet.