Brennan’s and rest of team's uncanny skills help resolve even grislier cases, including a retirement home murder, a possible death by robot, and the slaying of a close friend. Along the way, family tragedy strikes and Boothlands in the crosshairs of a serial killer. And a former Jeffersonian accused of murder kidnaps Brennan, prompting a shocking move by Booth.
The season was initially announced to debut in the fall, but Fox delayed the premiere until January 2017. Former series regular Eric Millegan, who returned in the season 11 finale, continues his role as Zack Addy in the final season. The season features the return of former recurring characters, including Eddie McClintock as Tim "Sully" Sullivan, who recurred during season two, and Stephen Fry as Gordon Wyatt, who made guest appearances in seasons two, four and five. Betty White reprises her season 11 role as Dr. Beth Mayer in the tenth episode, while veteran actors Ed Asner and Hal Holbrook guest star in the third episode. Filming of the season, and of the entire series, wrapped up on December 15, 2016.
When a tutor of privileged students turns up dead, the team sorts through all the possible perpetrators, from disgruntled parents to the tutor's roommate with a criminal record. Meanwhile, Bones is frustrated with the voice of her audio book and tries to prove that she can record it herself.
The dismembered body of successful golfer-turned-lumberjack Phyllis Paul brings the squints to the Lumber Sports Regional Championships. At this competition, Booth and Brennan discover numerous secrets that could have resulted in Phyllis' murder, including an affair with a married rival. Meanwhile, Hodgins secretly analyzes the bacteria on the bone of a prior victim that he believes will exonerate the murderer, Zack Addy.
When a series of corpses with ties to Booth's former Army unit appear around D.C., Booth must dive into his past to find the killer before the killer finds Booth. Meanwhile, Brennan's father, Max, hides a serious medical procedure from Brennan, leaving her to grapple with her father's trust and mortality, as well as her family being in danger.
When a young man dies in a horrendous hay baler accident, Booth, Brennan and Aubrey slap on trashy disguises and go undercover at a rowdy demolition derby competition to investigate the case. Meanwhile, Dr. Gordon Wyatt returns and assists Hodgins and Cam when the ongoing Gormogon case hits a dead end.
When the burning, bruised body of an aspiring writer/director crash-lands onto a passing car, the team investigates a series of odd locations and characters that are connected to his film. Meanwhile, Bones seeks guidance from Dr. Mayer on the meaning of passion in the work place and Booth allows Aubrey to take the reins on their current case.
In the series' penultimate episode, each leading character's final story begins to unfold. Brennan testifies for Zack in trial, Angela reveals some big news, while Aubrey and Jessica come to terms about their future together. All the while, the team discovers Kovac has escaped, leaving Booth in a race against the clock to protect himself and those closest to him from what may be Kovac's most dangerous plan yet.
With Kovac still at large, the team searches for evidence to track him down. After Brennan experiences a setback, the rest of the team must figure out how to find Kovac without her, putting everything she has ever taught them to the test. When all signs point to Kovac having outside help, as well as a hideout, Booth and Brennan go searching for him.