Brennan and Booth are called to an El Salvadaoran neighborhood on the outskirts of Washington D.C., after police apprehended JOSE VARGAS, a Latino Mara Muerte gang member. Upon routine inspection of Jose's trunk, they discover the unearthed remains of a female body. Numerous attempts by Brennan to communicate with Jose and the crowd about the location of the burial site prove futile. A black sedan speeds down the street with gang members opening fire on local law enforcement, as well as Booth, Brennan and Jose. Jose takes the opportunity to flee. A foot chase ensues, and Booth comes up empty as the suspect escapes over a chain link fence.
Back at the lab, Zack, Hodgins, Angela, and Brennan examine the bones and deduce the body was buried for roughly six months. Dental exam shows the victim was malnourished and is likely from a Central American country. A nerve is struck with Brennan over this unidentifiable female. She offers the woman's rosary to Goodman to be examined for religious iconography. The impact of the woman's demise resonates even stronger with Brennan as Zack shows a depression in the skull that indicates a baseball bat may have been the weapon of choice.
Booth interviews MIGUEL VALLEDA, "warlord of the Venganza Roja street gang," hoping to find a connection to the drive-by shooting. He threatens to hold the gang-banger on trumped up charges. Miguel mentions the irony in a drive-by where nobody is injured; but, the gang member escapes, implying Jose's own Mara Muerte gang committed the crime.
Brennan discovers the victim was five weeks pregnant. Hodgins learns from soil samples that the body was buried in fertilizer. Once he connects the fertilizer data with a "Loroco" flowering plant found in the same soil, the team determines a vegetable garden might be their impromptu cemetery. Brennan and crew set out to do a little "field work."
The team happens upon a local garden in the barrio. Hodgins finds a Loroco plant with the same maturity as the one imbedded in the victim. Brennan examines a fistful of soil with "Adipocere. It forms on the body in response to moisture from the ground" Trogid beetles that nibble on decomposing flesh, a partial rosary, and a freshly turned patch of dirt suggest they've found their grave site. An additional patch of adipocere in a different location offers the possibility of a "double homicide."
As Brennan saws a skull, Booth hypothesizes the police interrupted "a gang-banger moving the bodies of two murder victims." Brennan detects a head wound caused by internal bleeding. The weapon used in the crime left a mark on the skull. Hodgins finds evidence of an aquatic fauna typical of ponds and streams. The smoking gun comes from a rare flowering plant "that hasn't been seen in the wild since 1800." Only SENATOR ALAN CORMAN currently possesses such a plant.
Driving in Booth's vehicle, Brennan, Booth, and Hodgins brainstorm for possible connections. Hodgins tells the team that Senator Corman is a big supporter of business leaders in Central America. Indirectly, he's supporting regimes that use death squads to silence people who express opposition. These are the same people who flee to the United States. This could be a possible connection to the victim.
At Senator Corman's house, Booth, Brennan, and Hodgins quiz the senator about his association with El Salvadorian immigrants. It turns out they work for him on his property. Senator Corman does not recognize a composite sketch of Jose. A tour of the grounds reveals the same fauna found on the skeleton. The team meets the Senator's son, LOGAN, a landscape architecture student at Georgetown. The House Manager, HECTOR, doesn't recognize the sketch of Jose; however, Logan is familiar with his face. Two particular plants indigenous to ponds are discovered. This leads Brennan to the second victim's body.
Insect casings indicate second victim was a male who died six months prior to the first victim. Zack uncovers a "heart-shaped pelvic inlet" and "long projections of bone into the rib of cartilage." Goodman tells Brennan the first victim's rosary came from an El Salvadorian village called Milagro de la Paz. Angela completes a sketch of the woman. Zack finds a steel core, copper bullet in the bones -- It's the kind gangs like to use.
Brennan and Booth storm Jose's apartment. They see a picture of his family in Milagro de la Paz, the same village as the victim. A secret wall hides Jose's wife, Rosa, and their newborn baby. Booth tries to intimidate Rosa into giving information. Brennan's soft-side for the woman prevents Booth from any further strong-arming.
Angela, Zack, and Brennan examine the victims' bones. Both have a hole in the middle of their sternums unrelated to a gun shot wound. It's a hereditary condition that points to a father and daughter correlation. The team deliberates possible scenarios leading to the victims' deaths until Zack comes across a bullet in the father. Bone has healed around it, removing the notion that he died from a gunshot. Brennan inspects closer and sees, "marking on the floor of the acetabulum," a sign of "maetastic carcinoma." He wasn't murdered; rather, he died from prostate cancer.
After Brennan apologizes for caving in front of Jose's wife, Booth says he didn't need her info. He had the gang unit lean on Roberto Ortez, the leader of Jose's Mara Muerte gang. In exchange for a lesser charge on his sister, Ortez offered up Jose for questioning.
On a dark, city street, a car drives by and tosses out a body. We see that it's Jose. He has a note pinned to his chest: SPECIAL DELIVERY FOR AGENT SEELEY BOOTH, FBI.
In the hospital, Booth presses Jose about the victims. He threatens to have him and his wife deported, keeping his son in the states. Brennan scrutinizes Jose's X-ray and observes the same sternal foramen hole as the two victims. Jose is related. The victims were his father and sister. Jose is reluctant to provide any further information. At Brennan's request, he surrenders the names of his father and sister: Augustin and Maria Duarte.
Booth and Brennan grill the Mara Muerte gang leader, Ortez, about Jose. They learn Jose's sister did not care for her brother and the people he associated with. Ortez shares the same feelings for different reasons. Brennan confronts Ortez in the hallway. He is rude and suggestive. Brennan proceeds to level him with a series of tactical punches.
Angela reprimands Brennan for attacking a violent gang leader. Brennan reveals a story about her travels to El Salvador where she worked a case involving an executed girl. The girl was tossed in a well. Brennan was abducted by the local police for interfering with the body. She spent days in a jail cell, her life repeatedly threatened by military and local police. Hodgins interrupts her recount with information on the type of weapon used to kill Maria, a "Quarter-sawn cumuru." -- expensive wood used for furniture - the kind a senator might be able to afford.
The Senator denies any involvement in the killing. He's claims to never have seen the woman before, even though she was employed as a maid on the grounds. Hector, his House Manager, confesses that the Senator's son, Logan, had an affair with her.
They question Logan in his bedroom. He admits to the relationship, but acts surprised by the news of her death. Brennan discovers dried blood and skin on this bedpost. It's made from the same wood that killed Maria.
Logan and his attorney, NEIL CLAYTON, field questions from Booth. Logan answers against the wishes of his lawyer. He started a sexual relationship with Maria six months ago. When Booth makes him aware of her pregnancy, Logan becomes believably upset and distraught.
Angela and Brennan review the possible suspects. Due to the height of the bedpost, they rule out Senator Corman, Logan Corman, and Hector Santiago. The angle of impact does not match the heights of their suspects, even if she was lifted. And if she fell off a ladder, it would not be enough force to explain the damage to her skull. Brennan surmises she was yanked off the ladder by someone else. This would provide enough power to severely injure, if not kill.
Upon further questioning of Jose in the hospital, Brennan guesses his father died of cancer around the time Jose's wife was pregnant. Jose wanted his child born in America, so he buried his father himself, in the garden. Not being a citizen, he had no other choice. And when his sister died, he buried her in the same place. Jose joined the Mara Muerte to get fake papers to work for the Senator. Prior to his father's death, he swore he would take care of his sister. She never knew the truth.
Booth and Brennan return to the Senator's home where they recreate the scenario with the ladder in Logan's room. Trained in "Kinesiology," Brennan orders the Senator to pull her off the ladder. She will be able to tell if the angle and force would be an adequate match for Maria's death. The Senator complies and Brennan is not satisfied. When the House Manager, Hector, is asked to repeat the same motion, he hesitates, then refuses. Ultimately, he owns up. He told Maria she was not to be in Logan's room. When she disobeyed, he promptly pulled her from the ladder, causing her to hit her head. He gave her five hundred dollars to see a doctor, but she ignored his request from fear of deportation. Booth places Hector under arrest for manslaughter.
Booth is told at FBI headquarters that Mara Muerte has put a hit out on Brennan. Maria and her father have a proper burial in a cemetery, arranged by Brennan.
Booth encounters Ortez in an alley and threatens him with retaliation if Brennan is hurt by his gang. He shoves his gun in his mouth and makes it clear he will not think twice about killing him. Ortez agrees.
Jose and Rosa thank Brennan for the funeral. He vows to repay her. His family is moving back to El Salvador. Booth arrives "late to a funeral" and never divulges his run-in with Ortez. His actions were altruistic. He may have a heart after all.