On a golf course near Virginia Beach, Brennan and Zack pull up to the scene of a small plane crash. As members of the local fire department and F.A.A. investigate the wreckage, IAN DYSON of the NTSB informs Brennan and Zack that the private plane was a State Department flight, "with a bunch of V.I.P.'s on board." Due to the absence of Booth as their F.B.I. intermediary, Zack assumes an elitist role, condescending to the investigators at the scene. They discover "two skulls" from various fragments, bringing the death count to six, including the pilot and co-pilot. The bodies appear consistent with the composition of standard plane crash victims, "burned to a crisp" while "burst fractures of lower thoracic and lumbar vertebrae" appear "consistent with injuries caused by the vertical impact of the falling aircraft" That is, until Brennan unearths a "femur fragment" with "no charring remains." One of the victims was not aboard the doomed flight.
Brennan, Zack, Hodgins, and Angela sit on the receiving end of Goodman's top secret update. He informs the team that two "high-ranking" Communist Chinese trade attaches were on the plane when it crashed. It can be proved the plane was not shot down; rather, an accident, however, Zack and Brennan questions the six sets of human remains when the manifest listed only five people, one of whom was an American Businessman. The story begins to fall apart further when Zack reveals unusual cut marks on the bones "congruent with dismemberment." The State Department orders the Bones Team to identify the sixth body.
In the lab, Brennan brings Booth up to speed with the evidence: "piece of skull, chunk of a vertebrae, part of a femur." Booth questions why he should be involved in a case that isn't murder, insinuating Brennan simply missed him. Brennan disagrees on both claims, offering on the former that the body was "hacked." JESSE KANE, an expert in missing persons cases, enters the picture with knowledge that his father might be the extra pieces of bone found on the golf course.
Brennan and Booth listen to Jesse's plea for involvement in the investigation. He tells them his father "went missing five years ago during a trip to his cottage in Virginia Beach." According to Jesse, the investigation was bungled, but Booth does not buy it. In fact, Booth is more concerned over Jesse's awareness of the Chinese victims on board the plane. Brennan refuses to discuss the details of the case, but uses Jesse's information as leverage to convince Booth that murder, indeed, is at stake. Booth agrees to convince his superiors he should assist.
Zack, Angela, Hodgins and Brennan review the mysterious sixth victim's data in the Bone Room. Zack found "Nasal ridges" indicating "she was a Caucasoid female approximately 5 ft' 10. Epiphyseal fusion puts her age somewhere between twenty to twenty-five." Angela theorizes the victim could've been a mistress, or hired entertainment. Brennan focuses on the bone bits of the skeleton separated from the plane.
"Supraorbital margin is rounded, suggesting a male," Zack proposes. Brennan deduces the bones came from a "middle-aged guy" who expired five years prior, due to "...osteophytic lipping" paired with "weathering and discoloration." The team collectively decides to disobey Goodman's orders to make the "sixth victim" their only priority. They choose to pursue the male behind the bone shard as well. Hodgins is recruited to throw Goodman off their trail.
At a coffee shop, Brennan tells Jesse the bone fragments are the same age and sex as his father. She listens to his foray into the legal side of locating missing persons. Because of his dad's disappearance, and the resulting lack of interest on the part of the police force regarding his search, Jesse educated himself on motivating law enforcement through victim's rights. He attempts to bond with Brennan over the loss of both her parents. She sticks to business, mentioning Booth's interest in the obvious foul play evidence.
Zack, Angela, and Hodgins secretly review one of the three bone fragments not included in the plane crash. They are interrupted by a nosey Goodman who prods them to see if they are disobeying his orders, choosing to neglect the Chinese bodies for the stray bones. Hodgins rebounds, mentioning the linear, elliptical pattern of the cuts on the bones are too organized to be from a machine like a Chainsaw. The bones were cut, but not scattered and chopped by an orbiting saw. This is true of both sets of bones, the ones inside and outside of the plane. Goodman appears satisfied with their slight-of-hand investigative work.
Traveling in Booth's vehicle, Booth admits to Brennan that Jesse Kane has built a solid case around his father's girlfriend as suspect number one. KAREN ANDERSON has no alibi and "remains in the house" with "access to their joint accounts. By the time police officially declares Max Kane dead, she will have already siphoned off the lion's share of his net worth. Booth recommends interviewing Ms. Anderson to read her "subtle psychological indicators." Brennan points out that she's studied the body language of deception, but Booth cuts her off , "I don't poke around in the bone stuff, you leave the human stuff to me." Once again, she is faced with her need for Booth.
Booth and Brennan meet with Karen Anderson. She is reluctant to discuss the case from fear of implicating herself. She knows it looks bad, seeing how she lives in Max's house and has fallen in love with another man, Eddie. However, the scales tip when she discloses Jesse's estrangement from his father two years prior to the disappearance. Max cut off his son financially and criticized his lazy lifestyle. Jesse was "furious" with his father.
In the Bone Room, Zack, Hodgins, Angela, and Brennan quietly discuss their findings on Max Kane's alleged bones. Zack knows the "hack marks were caused by a heidel carving knife." Hodgins offers, "the osteological profile suggests evidence of post-mortem freezing," suggesting Max Kane vanished mid-winter. When added together, Zack paints a gruesome scenario, "the victim was frozen, dismembered, and then fed into a wood chipper." The team weighs the pros and cons of coming clean with Goodman about their secondary investigation findings. They settle on continuing their concealment.
Booth and Brennan interrogate Jesse in Booth's office. Jesse admits he was cut off from his father, adding he was a disappointment to him in many ways. Booth instructs Brennan to tell Jesse how the victim was processed by a wood chipper. Jesse is visibly distraught. Brennan softly informs him that they still aren't certain the victim's bones are positively Max Kane's. Jesse requests a viewing of the bone fragments, which Booth allows.
As Jesse looks over the fragments, he recounts his research in to his father's death. He "...met with a client at the NorthStar Grill in Virginia Beach. I know he had meatloaf. I know he was supposed to meet Karen at the pier but he didn't show up. I know she waited two days before reporting him." He offers a final tug on Brennan's heart strings by indicating how hopeless she must feel for knowing nothing about her parents' deaths.
n her office, Brennan shows Jesse the slim "missing persons" file on her parents. Jesse is amazed at the lack of material the authorities provided for her, pushing her to dig deeper on her own. Brennan believes in the system, a notion Jesse fervently refutes. Her beauty and passion get the best of Jesse as he leans in for a kiss denied. Angela interrupts the moment with a schematic comparing the skull fragments with a picture of Max Kane. The skull schematic conveys a "pretty good chance" the pieces belong to Jesse's father.
On the way to the Angelator, Brennan and Angela discuss the possibility of Brennan going on a date with Jesse. Brennan dismisses the thought, sighting his current status as a suspect. Once in the lab, Brennan, Angela, and Goodman study the holographic skeletal images of the plane crash victims. They identify both pilots as well as the two Chinese victims. There is a match with the photos because their, "Occipital orbitals line up and their "cranial meninges are in sync." Toxicology reports show the two Chinese nationals had "elevated levels of alcohol and Sildenafil - more commonly known as Viagra." The mystery girl, now labeled a "prostitute," also "showed traces of alcohol and cocaine." Zack mentions the "prostitute" had stress signs on the "cuboid" and "medial malleolus" bones in her foot, a sign of wearing "high stiletto heels." The team plans to match the images and data with pictures from escort services in the D.C. area.
Booth locates the only "Blackmantis 1200" wood chipper in Virginia Beach. Although Booth's guys couldn't find any blood residue, he figures Brennan's team can match the blades to the cuts on the bones. Only two people have had access to the wood chipper in the last seven years: City Maintenance Foreman, and a maintenance worker named Ray Sparks. Brennan asks Zack to run a "dispersal pattern test on the chipper," assuming the victim was frozen solid when he was "fed into the wood chipper."
At Ray Spark's house, Brennan lectures Booth on abusing Zack's friendship. Booth is comfortable with his power play over Zack. It's a guy thing. Ray refuses to answer the door, making a run for it out the back. He chooses poorly as he meets the unwieldy hand of Brennan, who apprehends him with a throat chop.
Zack and Hodgins set up the wood chipper in the Jeffersonian parking lot. They feed a frozen pig into the machine in order to determine the "dispersal pattern of the fragments." They aim to compare the pig fragments to the fragments found on the golf course to tell if the Blackmantis 1200 wood chipper was involved in the crime. Pig parts spray the crowd, along with a displeased Goodman.
Booth questions Spark in the interrogation room. He discovers Sparks knew Karen Anderson from the golf course, where he used to frequent for lunch. Booth puts the screws to him tighter, pressing about the fancy home where he resides. Sparks smugly responds that five years ago he was locked up in Southampton Correctional Center for a DUI, absolving him of any potential connection.
Goodman reprimands Hodgins for disobeying his orders. Hodgins challenges his threats with laughter whereupon Goodman's tone grows grave. He sends the message that he has no reservations in taking Hodgins down, even if it means "striking at you through your friends and co-workers."
Out of ideas, Booth continues to push Jesse to confess. He knows the simplest theory is usually the best, and in this instance, a disgruntled son worried about losing his inheritance is the most viable lead. Jesse appeals to Brennan's compassionate side. As someone who's lost a parent, he asks her to understand his need for "the truth."
Angela and Brennan examine a satellite image of the bone fragment displacement on the golf course. They surmise the chipper would most likely be aimed over the stream to wash the evidence away. A careful inspection of the course turns up an access road where a truck could've placed the chipper with the correct trajectory. Goodman inquires about their progress on the mystery woman. They tell him the woman is Caucasian. Satisfied, he instructs them to begin their work on the bone fragments. They all share an awkward glance, admission of their guilt.
Brennan goes to Jesse's hotel room to ask for the file on her parents. He reads her request as a sign she no longer believes in him. She lets him know his obsession with his father's past is unhealthy. He jabs back at her, asking how doing nothing could be healthier, as she has maintained for so many years.
The Bones team searches the golf course in the established pattern of the wood chipper. They uncover a number of additional bones, including a piece of finger with a nail still attached to it. Underneath the nail, they discover polyurethane, indicative of a victim "scraping at something before he died." An odd cell structure tips Brennan to the possibility of a "non-malignant bone tumor." She requests the most recent bone scans from Max Kane's medical records. The team is interrupted by a phone call from Booth. Jesse Kane has been arrested for attacking Karen Anderson.
Riding in Booth's vehicle, Booth informs Brennan that Jesse showed up at Karen's house to confront her. Her lover, Eddie, tried to throw him out. The two exchanged punches. Brennan asks Booth what his gut instinct is about Jesse. He admits he doesn't think Jesse is responsible. Brennan salts his wound by telling him the bone fragments from the golf course are NOT Max Kanes. Jesse is innocent.
Brennan tells Jesse the bones aren't his father's. "...A juxtacortical chondroma - a non-malignant bone tumor" was found, inconsistent with his father's x-rays two months prior to his disappearance. Brennan consoles him, knowing what it's like to "not know what happened." Booth offers to make the assault charges go away.
Team Bones heads back to the drawing board. They review the "pertinents" of the case and realize Ray Sparks is the only connection to the wood chipper. Although Ray Sparks was in jail when Max Kane disappeared, he could've been around for someone else's demise, namely, his brother's.
At Ray Spark's house, they discover a freezer with claw marks embedded in the lid, consistent with the polyurethane residue under the fingernail. Ray killed his brother.
Brennan informs Jesse of Frank Sparks undoing. She helps him wrestle with the grief of another dead end in the search for his father. When asked how she can live knowing nobody is looking for her parents, she replies, "There's a Zen koan that says if you want to find something, you have to stop looking for it." Jesse's obsessive nature is too powerful to accept that philosophy.
The team convenes at Wong Foo's where Brennan hesitantly asks Booth to review her parents' file. Booth proudly accepts. Zack engages Booth in a discussion that falls on deaf ears, a moment which makes him happy. Booth's silence proves Zack is still a member of a team bound by the unwritten code of men. Brennan regards Booth as she leaves the restaurant, catching him admiring a youthful photo of herself from the file.