The Grave Digger
10 episodes of Bones carry this thread, 10h in all — 3 of them are in The Essentials.
Arc membership is derived from each episode's own title and summary text. It shows where a thread is foregrounded, not every episode it touches.
In airing order

When high-school classmates reunite to unearth a time capsule buried 20 years earlier, they find the corpse of an adolescent friend inside; while combing through the victim's life, the team members rehash their own teen years.

Brennan and the team get a phone call from the Grave Digger, who informs them that Booth has been buried alive with only 24 hours of oxygen.

The body of a pregnant 16-year-old athlete found buried in a mound of salt in a city de-icing truck leads Booth and Brennan to the discovery that many of her teammates are pregnant or have babies after a pregnancy pact.

Angela's psychic, Avalon Harmonia, reveals while reading Angela's tarot cards that there are multiple bodies buried under a Washington, DC fountain.

The trial of The Gravedigger hits close to home for members of the team, and everyone at the Jeffersonian must work overtime to uncover the forensic evidence to elicit a conviction.

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 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. Meanwhile, Sweets attempts to put on a brave face after being caught in the firestorm just moments following a chilly encounter with The Gravedigger.

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. Meanwhile, Angela's father visits the Jeffersonian and insists on naming his unborn grandchild.

The Jeffersonian team investigates the murder of Lauren Frank, a kidnap victim whose remains were found buried at a park. But when they discover the unhappy relationship that Lauren had with her stepmother, the team starts to think the killer was someone closer to the girl than expected. Meanwhile, Hodgins uncovers a shocking secret about his family and Brennan and Booth face a common couples dilemma - whether to co-mingle their funds -.

To produce a television segment on the Jeffersonian's Medico-Legal lab, a documentary crew follows Brennan, Booth and the Jeffersonian/FBI team on a "typical" case as they investigate a corpse found in a landfill that was buried there more than a decade ago. The camera captures normally unseen footage of the team at work, while candid commentary by each of the team members provides an inside look at the investigation as Booth and Aubrey show off their unique skills in the field, and Brennan and her team prove their expertise and integral importance to solving murder cases.