When a routine necropsy of a black bear in rural Washington State turns up a human arm, FBI sends the case to Special Agent Seeley Booth in hopes of getting forensic anthropologist, Dr. Temperance Brennan, to ID the victim. Uncomfortable with being at anyone's beck and call, Brennan is at first reluctant to go until she is ordered to do so by her boss, Dr. Goodman who feels, if for nothing else, it will get her out of the lab and into the world to "connect with other people." Brennan concedes. She examines the arm bones and is shocked to find kerf marks and residual cross-section striae - cut marks made by a saw on the bones. A person cut off this arm before the bear ate it.
Brennan and Booth make the trip to small town "Aurora" Washington (pop. 3826) to investigate, engaging the help of locals in a place where everyone knows everything about everybody. While Booth meets with the Sheriff Scutter, Brennan examines the bone fragments with local doctors and determines the arm belonged to a young male who was well muscled but the only person reported missing thus far is a woman - Ann Noyes. Sheriff Scutter, unimpressed by the FBI, immediately takes to Brennan, much to Booth's annoyance. Brennan, however, is entirely unaware of the attention she is drawing as she engages the help of a flirty UPS guy, Charlie, to ship bone fragments back to her lab. Zack debrides them and finds unusual indentations. He satellites these images to Brennan and she ascertains that these are bite marks -- not from a bear, but from a human. Brennan realizes, to the horror of the local residents, they don't just have a killer in their town. they have a cannibal.
Brennan realizes a cannibal would get sick with prion disease, and goes to confer with local doctor/coroner Dr. Andrew Rigby - a man who is also smitten with Brennan and eager to help. Unfortunately, he has not come across patients with such symptoms. Back at the lab, Hodgins examines the bear scat that Brennan shipped to him and finds in it a metacarpal, a sporocarp, and a layer of dermis with pigmentation marks in the microphage - a flap of skin with a tattoo. Angela artistically recreates the tattoo and realizes it's a Haida Sun motif. With that piece of evidence, the Sheriff runs a new missing persons check and finds a match: Adam Langer, 22, missing 10 days from a nearby college. The Sheriff realizes he knows Adam - he used to come up to Aurora to visit Sherman Rivers, the town's Native American Park Ranger. When Booth and Brennan pay a visit to Ranger Rivers, he runs, escaping into the woods. Booth gives chase, but loses him when his flashlight dies leaving him in the dark.
Brennan and the Sheriff search Ranger River's cabin and find a half-eaten apple and some strange looking meat. Brennan ships it all back to her lab. In the meantime, Hodgins has figured out that the sporocarp is a tuber gibbosum - an Oregon white truffle that only grows in symbiosis with Douglas fir trees. He shaves the truffle, finding boring dust produced by beetles. This means the tree the truffle grew on was infested. The next day, Booth, Brennan and the Sheriff are able to find Ranger Rivers in the woods -- he says he only ran because "Indians and the FBI don't mix." Zack has figured out that the meat samples from Rivers' cabin were all black bear and that the teeth marks on the apple don't match those on the bone fragments - he's not the cannibal (although he is a poacher). In exchange for getting off the hook for poaching, Ranger Rivers leads them to the infested stand of trees in the woods, where they find a perverse version of a Medicine Wheel and two dead bodies - Adam Langer and Ann Noyes, the missing hiker, who's also missing her heart.
Brennan and Dr. Rigby do autopsies on the bodies, both of which were killed by gunshots to the head. Based on adipocere formation, Brennan estimates Ann Noyes has been dead for about a week. When Ranger Rivers reveals that Adam Langer had been seeing local veterinarian Dr. Denise Randall, Booth and Brennan pay her a visit, getting her to write into a block of dental medium so they can check her teeth marks -- but, as Brennan points out, even if she killed Adam Langer, why would she have killed Ann Noyes? And is she really a cannibal? They are more likely looking for someone who's clinically insane. Word gets around fast and everyone in town is speculating on the case; the men have Brennan in sight as she starts to realize just how good "connecting" with others can feel.
Back at the lab, Zack examines photos of Ann Noyes's sternum and finds more tooth marks -- only these are made by a machine, not a person. He beams Brennan the images and she figures out they were made by a sternum spreader -- which is the clue that ultimately helps Booth and Brennan figure out the case and catch the cannibal.