The team works to uncover clues buried under a life’s worth of possessions saved by a hoarder in order to solve the mystery of his death. Meanwhile, Angela’s father has a specific purpose for his most recent visit, and Brennan and Booth are confronted with unique opportunities.

The trial of The Gravedigger — the serial killer the team finally caught last season — has arrived, and the team must work hard to find enough evidence to guarantee a conviction.

Two bodies are found in the woods — one belonging to a modern-day witch and one that is over three hundred years old, dating back to the time of the Salem Witch Trials. As Booth and Brennan go in to investigate, Angela and Hodgins meanwhile end up in jail.

When the body of a rich adventure-seeker is found in a hotel laundry machine, Booth and Brennan are led to the last place he was seen: a Rock ‘n Roll Fantasy Camp. While Brennan and Booth lead the investigation outside the lab, Hodgins, Angela and intern Arastoo use a fragment of prehistoric wooly mammoth tusk – found with the remains – and Angela’s knowledge of the music industry to connect the evidence to potential suspects.

When human remains are discovered in the belly of a shark, Brennan and Booth are brought in to identify the missing person. Evidence suggesting the victim had been the prey of several fish directs the team’s investigation to The Aquarium of the Atlantic, where a guest lecturer and notorious self-help guru preaching the healing power of the ocean has gone missing. Meanwhile, both Brennan and Booth navigate their own relationship when a marine biologist shows interest in Booth

The team’s latest case takes Brennan back to her alma mater where she and Booth investigate the discovery of an unidentified skull and upper torso. With Angela’s help, they identify the victim as one of Brennan’s classmates, and notice a possible connection to a second murder committed 15 years prior.

In the 100th episode, Bones looks back at the first time Booth and Brennan worked on a case together. The formation and evolution of their relationship, as well as the relationships of the other Jeffersonian workers, is examined.

When a subway train is thrown off the track by 60,000 gallons of flood water, a partially skeletonized body emerges out of the overflow. While Dr. Sweets, a passenger on the derailed train, copes with post traumatic stress, the rest of the team and intern Daisy Wick get to work on identifying the victim as Martin Aragon, a professional ghost writer caught up in a deadly love triangle. Meanwhile, Brennan releases her second book to great success, but has to accommodate a nosy reporter, and Sweets’ near-death experience leads him to make a drastic decision.

Booth and Brennan examine disfigured remains that oddly relate to biblical text. They discover that the victim was a patient at a sanitarium, and have trouble sorting through the list of suspects they uncover.

Booth and Brennan are called in when a skeleton is found in the trenches of a Civil War battleground. Brennan determines that the remains are those of a present-day dentist, but a residue stuck on the bones is keeping the cause of death from being determined. Meanwhile, Booth’s brother Jared returns with interesting news.