Booth and Brennan are in the office of their new therapist, Dr. Lance Sweets, age 22. Ignoring Booth's ridicule of his young age and Brennan's disregard for psychotherapy in general, Dr. Sweets attempts to evaluate whether or not the partners should be separated. He gives them a take home test to help in his assessment.
Booth and Brennan are driving back from the therapist's office when the call comes in that a body has been found.
The partners arrive at the Veterans Administration Hospital, an abandoned building where teenagers now gather on the weekends. Cam greets Booth and Brennan and leads them to the body. The carcass looks as if it's been decaying for at least a few weeks, but in such a high traffic location, it should have been discovered much earlier. Brennan notices that the body still feels warm, so Cam takes a reading of the body's internal temperature. It comes back 127 degrees. The body was cooked.
The body's been brought back to the lab where Brennan, Hodgins, and Zack look it over. Zack thinks he's found a bullet hole in the sternum, but the squints are having a hard time getting a clear view of the remains, as they've been exposed to a heap of mud and debris. While separating the particulates, Hodgins comes across a bug from the Nitidulidae family. He's pretty excited, as he's never found one on a body before. Cam enters as Hodgins comes across another odd discovery: a heavy concentration of dead bristletails and harvester ants near the victim's feet. He takes a clipping of the victim's pants cuff for further testing.
Booth shows up in Brennan's office, where Brennan is working on her psychiatric take-home test. Booth tries to peek at her answers. Angela arrives with an I.D. on the body: the cooked carcass is Franklin Curtis, the middle-aged owner of a nationwide, organic supermarket chain. Hodgins enters. He's just tested the fabric on Frank's pants and found pesticides on them: pretty strange for a man who devoted his career to selling organic food.
Booth and Brennan are at the Curtis farm where they speak with Frank's wife, Margie, and daughter, Kat. Margie tries to tell the partners how well loved Frank was, but Kat gives them the truth. Frank pressured other farmers into going organic, siccing his team of lawyers on any farmer who resisted. He always found a way to buy the farmers out, and made plenty of enemies by forcing people off their land. Booth wants to know if, at the time of his death, Frank was trying to convert any farmers.
The search leads Booth and Brennan to the tobacco farm of Andrew Harding. Harding is clearly no fan of Frank Curtis, and he's having a hard time rallying any sorrow for the man's death. Booth tells Harding that Chloropicrin was found all over Frank's body. Chloropicrin is a pesticide that Andrew Harding used on his farm, the day Frank went missing. Harding comes clean. Frank did show up at Harding's farm that day, and Harding may have "accidentally" sprayed him with the chemical hose.
While driving, Booth and Brennan debate the issue of pesticide-grown versus organic produce, with Booth noting, "you're not going to see me paying four dollars for a tomato." Brennan fires back with data on a study done on alligators swimming in pesticide-infested water: They "have smaller genitalia than their clean-water counterparts." Booth takes this in.
Back at the lab, Cam shows Angela some indentations found on the body. Angela is able to identify the marks as those made from buttons, as if buttons were pressed into the victim's decaying flesh. The only problem with this theory is that the clothing Frank was wearing at the time of his death didn't have any buttons.
Back on the road, Booth and Brennan continue their debate. Suddenly Brennan has a realization: tobacco needs to be cured, and it's done so in curing barns. Harding would have been able to cook Frank's body. It's enough to get them a warrant to search the farm. Cam calls Brennan with news of finding "skin-slippage" on the victim. She's discovered that Frank wasn't alone in when his body was cooked. A second victim's skin had melted onto his. They need to find that other body.
Booth is back at the Harding's tobacco farm. FBI agents search the farm as Booth speaks to Andrew and his wife, Lizbeth. Lizbeth tells Booth that Frank Curtis was a big flirt. Frank thought he could charm Lizbeth into convincing Andrew to sell the farm. Apparently Andrew was infuriated at learning this. Booth thanks Lizbeth for her help.
Hodgins and Zack are in the lab discussing the ways they choose to help the environment. Hodgins has finally identified the full name of the bug he discovered earlier: it's a Carpophilus Nitidulidae, which, interestingly, is usually found on pineapple plants.
Back at the Harding farm, Booth speaks with an FBI Forensic Tech. The Tech tells Booth that the curing shed is clean. They've got nothing. Booth gets a phone call: it's Brennan, back in her office.
Brennan and Angela speak with Booth over the phone. They know Frank was around pineapples before he died. But the closest pineapple grower is in Florida. Angela mentions reading an article about a farmer who's attempting to grow tropical fruits in a hothouse in Virginia.
Booth and Brennan go to the Page farm, where they speak with Lyndon Page, the man from the article. Lyndon is indeed growing pineapples in his hothouse. But Lyndon claims to have never had a problem with Frank. He jokes that the reason they never fought is probably because Lyndon didn't have a wife for Frank to hit on.
Booth and Brennan check out the hothouse. It's filled with pineapple plants. Booth airs his frustration over Dr. Sweets, who's clearly a former high school nerd trying to get even with Booth for being a jock. The two are interrupted by the overwhelming smell of the nearby community composting facility. Lyndon tells Booth and Brennan the facility takes in agricultural waste and in return gives the farmers certified organic compost. This gives Brennan an idea. She grabs Booth and they head off.
While driving, Booth and Brennan speak with Hodgins over the phone. Hodgins tells them that a compost heap could heat up to 170 degrees, high enough to cook a body. When Hodgins hears that Brennan and Booth are going to check out the compost pile, he wants in.
Booth and Brennan are at the compost facility where they speak with the manager, Gavin Lee. Gavin gathers Tim Peck and Clay Ansley, a couple of local farmers. Charlie Rogan, a facility employee, approaches with news of the facility's only truck breaking down again. It's been acting up ever since they switched it to biodiesel fuel.
Booth takes the opportunity to question Charlie about Frank, and it turns out Charlie knew the victim very well. He dated Frank's daughter, Kat, all through high school. Charlie thought Frank Curtis was a great man. Clay disagrees with that assessment, saying Frank was only in it for the money. He cites Frank's huge house and constant air condition usage as proof of his disregard for the environment. Booth wants to close the facility and search the compost for the second body, but Gavin tells them he won't do it without a warrant.
Booth and Brennan are back at Dr. Sweets' office. Booth is distracted as he waits for the warrant. Sweets attempts to have the partners talk about conflict, which sparks an argument between the two. Sweets thinks he's finally getting somewhere with them, and he tries to lead Booth in a visualization exercise. It doesn't work. Booth gets a call: the warrant is in place. The partners leave the frustrated therapist.
In the Bone Room, Zack shows Cam his findings. Fractures and bone bruising around the femur and the left ulna suggest Frank Curtis was in a fight before his death. And what was originally thought to be a gunshot wound to the sternum is revealed to actually have been a congenital abnormality. In addition to that discovery, Zack has found "multiple puncture wounds with hinge fracturing on the scapula and posterior aspects of several ribs." The victim was stabbed.
Booth arrives back at the compost facility, where Brennan and Hodgins are knee-deep in fertilizer. Booth is frustrated that the facility doesn't use video surveillance. He has no way of narrowing down his long list of suspects. While working, Hodgins hears a crunch under his foot. They lift a layer of mulch and discover another decomposing body. It's the body of a young woman, who appears to have died around the same time as Frank Curtis. "Even dead, old Frank was lying with another woman."
Back at the lab, Zack and Cam examine the second body while Hodgins studies his samples. Hodgins determines that the woman was actually killed the day before Frank, was which raises the question: assuming the two victims were having an affair, "who catches two people cheating but kills them a day apart?" Angela enters with her composite drawing of the newest victim. She's had no luck matching it to anybody in the missing persons database. Injures on the body, cracked ribs and a fractured sternum, lead the squints to conclude that somebody tried to use CPR to save this woman from dying.
Booth is back at the Curtis farmhouse, where he again speaks to Frank's wife Margie. Margie admits to knowing about Frank's affairs. Booth thinks she stayed with Frank for the money, and maybe even murdered Frank and his current mistress to get the insurance money. Booth wants to know why Margie didn't tell him about Frank's affairs the first time they spoke. She says she was protecting Kat. Kat then enters, along with Charlie. She tells her mother that she knew of her father's affairs. For that matter, everybody knew, but Kat pretended not to for her mother's sake.
Booth shows up in Brennan's office with the news that Frank had kept an "office" in town. And that "office" was actually an apartment, which Frank Curtis presumably used for his trysts.
Booth and Brennan arrive at Frank's apartment. They investigate the place as a potential crime scene. Brennan notices something distinctive: a pair of sunglasses with bamboo frames. Booth thinks those sure seem like something Frank would own, but the place looks as if a woman was staying there.
As Brennan shines an ALS over the room, she comes across dried blood on the coffee table. Brennan wants the contents of the apartment moved to the Jeffersonian for further analysis. Booth finds a take-out receipt. The name on the credit card used is Emma Billings. Brennan, in the kitchen, has found a photo of what looks to be Frank and Emma together. Emma is an identical match to Angela's victim composite.
Brennan and Zack are in the Bone Room, where they have the body of the second victim and the coffee table displayed. Together they try to hypothesize what could have happened. Cam enters with some background on Emma. She was a cashier at one of Frank's stores in New Jersey. Cam believes Emma came to Virginia to hide from a stalker: a guy named Noel Liftin. Emma had a restraining order filed against Liftin.
Brennan tells Cam that it looks as if Emma's death was accidental: she hit her head against the coffee table and broke her neck. But Frank's death was definitely a murder, and they still have no leads on the weapon used: a thin, curved weapon, capable of multiple deep stabbings. Brennan gets a phone call from Booth. He's got Noel Liftin, who's been staying in a motel right across the street from the apartment where Emma died.
Booth has Noel Liftin in the interrogation room. Noel, acting very upset about Emma's death, thinks Booth should speak to Frank Curtis, seeing as how Frank treated Emma as if he owned her. Noel seems to have no idea that Frank is dead, too. But Booth isn't convinced, and Noel's alibi for those two days the deaths took place is a weak one: he was out selling hemp-oil body products door to door.
In the lab, Brennan and Hodgins look over a chemical diagram. Hodgins has found traces of some sort of vegetable oil in the furniture and carpeting of the apartment. It could be hemp-oil. Brennan wants Hodgins to re-examine the clothing of the victims in search of the oil.
Cam and Zack call Brennan into the autopsy room where they've made a major advance in the case. The two victims "shared a congenital abnormality" of the sternum, which prompted Cam to run a DNA comparison. Frank and Emma weren't lovers; they were father and daughter.
In the Bone Room, Brennan, Angela, and Zack hover over the bones of Frank Curtis. Zack is frustrated as he has tested countless knives and other weapons without finding a match for the murder weapon. Angela brings up a three-dimensional version of Frank's chest. Brennan has Angela widen the distance of Frank's shoulders on the screen. It becomes clear that the wounds were caused by a single blow from a multiple-tined instrument. A pitchfork, Zack concludes. Hodgins enters with the results of his oil tests. Brennan was right, the same oil appeared on both of the victims' clothing, but it wasn't hemp-oil. It was biodiesel fuel.
Booth, Brennan, and Angela drive. Booth's idea is that Noel, the creepy stalker, was watching the apartment Emma was staying in. Hopefully he'll be able to give them a description of whoever went into the building. From the description, Angela should be able to put a picture together. Booth thinks the killer was someone from the composting facility, since they use pitchforks to turn the compost, and biodiesel in their truck.
Booth, Brennan, and Angela arrive in the interrogation room, where Noel is chanting to calm himself. Booth wants to know about any suspicious trucks in the area during those two days when Emma and Frank died. Noel confirms that a truck from an organic composting facility arrived at the apartment complex at 4:37 last Wednesday, the same day and approximate time Emma was killed. Booth is able to extract more from the stalker: Noel saw a guy in his twenties leaving the truck, a guy with dirty blonde hair and bamboo-framed sunglasses.
Booth and Brennan are back at the compost facility. Brennan is measuring pitchforks and spraying them with luminal as Booth shows Gavin the bamboo-framed sunglasses. Gavin tells Booth that the glasses belonged to Charlie Rogan. They were a gift from Frank Curtis. Brennan pulls a pitchfork from the tool shed. It's the murder weapon. Charlie arrives, and is placed under arrest for the murders of Frank Curtis and Emma Billings. Just then, Brennan gets a call from Cam. She tells Cam the news, but Cam's got news of her own. DNA from underneath Emma's fingernails has been recovered. Charlie didn't attack her; Emma's assailant was a female. The DNA also showed a twenty-five percent commonality. Emma was killed by her half-sister, Kat.
Booth and Brennan sit with Kat in the interrogation room. Kat Curtis admits to killing Emma, but swears it was an accident. She just meant to scare the girl she assumes was sleeping with her father. The two fought, and Emma fell, hitting her head on the coffee table.
Charlie replaces Kat in the hot seat. He tells Booth and Brennan that Kat called him right after the accident. Charlie wanted to help Kat, so he got rid of Emma's body. The next day, Frank showed up at the apartment and saw the sunglasses Charlie left behind. Frank confronted Charlie at the compost facility that same night. Charlie was turning the compost. And as Frank charged, demanding to know what happened to Emma, Charlie stabbed him.
Kat tells Booth and Brennan the reason why she and Charlie moved her father's body. It was for the insurance policy for Kat's mother; there's no payout without a body. Frank had left most of his estate to charities in his will; Kat didn't want her mother to be penniless. Brennan tells Kat the truth. The girl she killed was the product of one of her father's long-ago affairs. She was Kat's half-sister.
Later on, in Dr. Sweets' office, the gloomy partners are seated before the young doctor. Sweets wants to know why they're so somber. And Booth explains to him "sometimes even if you win, you get left with someone else's pain and screwed up life." Sweets pries for more, and Brennan stops him in his tracks. She sticks up for Booth and their partnership. Dr. Sweets has picked up on just how well the partners complement each other, as evident on their tests. But over the next few months they'll still have plenty to work on. Sweets has decided to keep the partnership alive, but there are some deep underlying issues he's observed and those issues are going to be addressed.