The team helps Cam solve the case of an unidentified boy; after making personal discoveries, the members of the team realize they belong in Washington, D.C.

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.

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 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.

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 for her health.

The past and present collide when human remains from a 150-year-old slave ship, the Amelia 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 Amelia 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.