From all over the world Brennan's former team reassembles to help Cam solve a difficult case of identifying an unknown baby's corpse, as her failure to do so may wreck her career. They soon realize this may not be just one case, but two.

When the remains of a couple are discovered in a cave at National Park, the team must piece together the identity of the man and the woman as well as solve the crime. After interrogating two viable suspects, the team identifies the woman as a marketing executive who also served as her partner's AA sponsor, providing clues that lead them to expose the truth. Meanwhile, Booth's girlfriend and Afghanistan war correspondent, Hannah Burley, makes a surprise visit. After meeting Burley and sensing the couple's genuine happiness, Brennan re-evaluates her own relationship with Booth, and he tries to teach her that love is not always logical.

When Booth and Brennan are called to investigate decomposed remains found at the Jersey Shore, the team IDs the victim as Richie "The V" Genaro, a 23-year-old who partied the night before at a popular nightclub. Booth and Brennan question Genaro's peers including self proclaimed girlfriend Marie Galasso and the club bouncer, and Brennan surprisingly proves her pop culture savvy and anthropological expertise after watching what she believes to be a documentary on the inhabitants of the Jersey Shore, but was in actuality a reality show set there. Meanwhile, at the lab, the team grows fond of Booth's girlfriend, Hannah, and Angela tries to keep her pregnancy a secret

After a skull and decomposing hands are found in a dumpster, the team must not only solve the crime but also search for the rest of the victim's remains. Identified as Ray Raminsky, the victim turns out to be a bounty hunter in search of Charles Braverman, a man indicted for the murder of a co-worker. Meanwhile, Brennan is asked by Professor Bunsen Jude "The Science Dude" if he can shoot an episode of his children's show from The Jeffersonian Lab with Brennan as his special guest. Brennan initially turns him down, but is surprised when he makes her a deal she can't refuse, so she takes him on as a new "squintern." As the team pieces together the details of the crime, they discover that they are not alone in the hunt for Braverman and find themselves in a chase with an unexpected suspect.

On an isolated construction site, a skateboarder falls over a bump in a concrete slate - part of a young man's skull, identified from a rare dental tattoo as missing former ballet dancer Michael, who left the art to join street hip-hop art at a park with magician Johnny Wizard's informal, yet surprisingly competitive gang. The team follows a mold trace. Booth is however no less preoccupied by the safety of his lover, White House correspondent Hannah Burley, whose investigation for petty police corruption in D.C. proves physically dangerous.

The past and present collide when human remains from a 150-year-old slave ship, the Amalia Rose, surface. The team is tasked to give the deceased a proper burial but make an unforeseen discovery linked to a recent murder. In the course of the investigation, Booth and Brennan are led to a different kind of ship - a "Cougar" cruise - where they learn their victim was seen moments before his death. Meanwhile, Sweets struggles to maintain a casual relationship with Daisy, and Cam discovers a surprising and emotional connection to the Amalia Rose.

When human remains are discovered in the world's largest chocolate bar, a "sweet" event for a candymaker quickly turns bitter. As eccentric chocolate factory owner Jimmy Walpert deals with the tragedy, the team soon discovers that the victim was a mysterious character whose past is full of secrets, lies and love affairs. Meanwhile, Cam struggles with her daughter's decision to attend a university that fails to meet her high standards, and Hodgins asks Angela to arrange a party to announce her not-so-secret pregnancy.

Booth and Brennan's next case leads them to a crime scene where a human carcass has literally melted into the dashboard of a charred truck. As the team investigates the case, they discover a gunshot wound in the victim, but learn that neither the fire nor the bullet was the cause of the victim's death. Additional clues lead them to a local high school where the victim's wife is a teacher. As a student-teacher relationship begins to surface and a pattern takes shape in the lab, the team is able to track down the murder weapon and solve the crime. Meanwhile, Sweets resists the temptation of allowing his feelings for Daisy to interfere with helping her pass a government psychological evaluation, and Hannah attempts to break the ice and warm up to Booth's son Parker.

The Jeffersonian team finds a body in a tree and Dr. Brennan discovers that the victim is practically a clone of herself.

An unidentifiable body is discovered in the shower of an upscale home belonging to a young female socialite. With the help of nosy bones expert and Jeffersonian "squint" Clark Edison, skeletal reconstruction and evidence in the drain reveal that the victim was a young girl employed by a counterfeit handbag distributor. The team learns that the victim supplied counterfeit purses to her socialite acquaintance, and after interrogating the self-centered socialite and sifting through footage on a hidden camera, they discover evidence linking them to the murderer. Meanwhile, Angela and Hodgins discuss their future home and where they want to raise a family, and Booth opens up to Hannah about Brennan's feelings for him.

The city anxiously anticipates the arrival of Heather Taffet, more notoriously known as "The Gravedigger," for her final appeal after being sentenced to death for a kidnap-murder and a series of similar coldblooded crimes. But when a bullet targeted at The Gravedigger is fired from a distance and hits her, the Jeffersonian team is tasked to piece together the sniper's precise location as well as identify the suspect and his motives. With the help of probing investigator Caroline Julian, Booth and Brennan put together a list of likely suspects, but the evidence and the remarkable skill needed to pull off the crime leads the team to believe that the crime was an inside, professional job, leaving Brennan's father Max and even Booth as plausible suspects. Meanwhile, Sweets attempts to put on a brave face after being caught in the firestorm just moments following a chilly encounter with The Gravedigger.

A body disguised as a scarecrow is found with a bullet wound in a remote cornfield, and the team is forced to work against the clock to avoid a storm and potential complications that would affect the evidence. Booth and Brennan interrogate the victim's three wives, who are also sisters, and learn that jealousy between the sisters and their desire for their husband's attention had caused a major rift in the family. Booth and Brennan also question one relative who disapproved of the victim's polygamy. Meanwhile, Cam loses confidence in her relationship with her on-call doctor boyfriend, but they both realize they need to make their relationship a priority.

A BMX rider's remains are discovered on the roof of a warehouse after a failed bike stunt. While Booth and Brennan interrogate the victim's fellow riders, Hodgins and newly mellowed "squint" Fisher identify the numerous fractures in the victim's skeletal structure, and Angela recreates the series of events that led to the fatal accident. Meanwhile, Sweets turns to Booth for advice about his relationship with Daisy, and Booth makes a decision about his relationship with Hannah.

The liquefied remains of a wedding planner are found in her home tanning bed on Valentine's Day, and Cam pressures her team to solve the case in time so she can celebrate the holiday with her boyfriend. While the "squints" works tirelessly in the lab, Booth and Brennan interrogate a slew of possible suspects until they unlock classified files in the victim's computer, which lead to their main suspect. Meanwhile, Booth and Brennan downplay the significance of Valentine's Day, and Hodgins tries to plan a romantic day for Angela, but "squint" Clark helps him realize that the most meaningful gifts come from the heart.

After notoriously murdering "The Gravedigger," sniper-on-the-loose Jacob Broadsky strikes again. This time, his victim is a prior suspect who escaped the justice system. More determined than ever to catch Broadsky, Booth uses his own military training to beat the sniper at his own game. He vows to go to any lengths necessary to ensure that justice is served. In a heated and dramatic face-off, Booth has minutes to catch Broadsky before he hits an intended target, but Broadsky's skill and speed may prove to be a worthy adversary. Meanwhile, Angela's father visits the Jeffersonian and insists on naming his unborn grandchild.

A severe blizzard causes a city-wide blackout, adding to the obstacles the team must overcome in order to solve a murder case that could be linked to a potential viral outbreak. But when Booth and Brennan find themselves trapped in an elevator during the power outage, Sweets is on hand for outside assistance, but does more than what's asked of him when he initiates a touchy conversation about Booth and Brennan's relationship. Meanwhile, Angela and Hodgins get worrisome news about the health of their unborn baby, and Hodgins and "squint" Wendell Bray get creative in the lab and put their scientific skills to use to identify the victim and the rare disease.

Eight pairs of dismembered feet wash ashore after a recent flood on the U.S.-Canada border, but things don't add up when seven pairs of feet are identified as research corpses from a nearby university body farm. When Canadian forensic podiatrist Dr. Douglas Filmore takes the remains back to Canada, he and Brennan form an alliance to match the pairs of feet and identify the victim, and a rare and expensive pair of sneakers leads the team to the victim's murderer. Meanwhile, Cam gets in hot water when she makes college plans for her daughter behind her back.

A TV show host who systematically exposed fraud and superstition is killed in a forest where he intended to disprove the existence of the Latin-American mythological 'goat-thief', at first sight in the way the fable creature strikes. Suspects include parties he exposed but also professional rivals. Booth patiently sits through Bones' pitiful attempt to practice humor and welcomes her explanation for his sole 'cryptozoological' encounter with an apparent yeti. Vincent's confessions and apologies as ninth AA program step somewhat shock his Jeffersonian colleagues.

Sam Nozik's beetles-eaten corpse in a Florida glade is identified from his acrylic eye. He worked in a Miami museum, from which a treasure map to a Spanish galleon was stolen. Booth grudgingly allows his superstitious former foreign army tour acquaintance Walter Sherman (and his team of two) to use his 'tracing gift' to find and retrieve the treasure. They do, after consulting bishop Edward Galano on period navigation, and find the corpse, but meanwhile the diver herself has been murdered too. Booth meanwhile comes to terms with his grudge against Walter as 'insensitive' MP.

Award winning ad man Ross Dickson's corpse is found by prancing youngsters, buried in a public playground, beaten to death in a mysterious way. He was a member of a radical truth-society, which caused many conflicts in private and professional life. Encouraged by Bones, Wendell Bray follows his example to secure the extra hours only he needs desperately while Camille would divide them indiscriminately, a one-off success while the others explicitly prefer 'civilized untruthfulness'.

A mysterious young deaf girl is thought to have committed a recent murder after she's found on the streets, covered in blood and holding a knife. It's up to the Jeffersonian team to figure out who this girl is and determine if she's really the one to blame for the murder.

The search for Broadsky intensifies as he manages to kill one of the Squints. Angela and Hodgins name their baby. Booth struggles to protect those closest to him, which leads to an unexpected situation.

A generally disliked member of Max Keenan's bowling team's corpse is found as a decomposing mess in the cones machinery when that renovated section is reopened, but he was knocked dead a week earlier. Booth, good at the game, and Bones go undercover as new team members to study players and staff, which yields lots of grim grudges. Wendell has a hard time standing in, with online assistance, for Angela, who finally gives birth.