At a traffic stop, Booth is explaining to Brennan why the FBI is getting involved with something as mundane as a traffic stop: dodgy El Salvadoran neighborhood, Virginia plates, RICO, suspected drug dealer… it’s just messy all around. Especially when they find the decomposing body in the trunk. Brennan says it’s a female, recently dug up. The car’s driver, who has a gang tattoo on his neck, isn’t talking, and neither are any of the bystanders. Suddenly, a drive-by shooting interrupts the investigation and the driver takes the opportunity to run away. Booth chases him, but apprarently this guy can climb fences better with his arms handcuffed than Booth can with both hands. I mean, really.
Back in the lab, Zack says that the woman was buried for six months and that she was originally from Central America and was malnourished at the time of her death. A partial rosary was also found on the body and Brennan sends that to Dr. Goodman for him to investigate. The case really seems to get to Brennan, who gets teary as she says that the victim was religious. She should have had a casket and a headstone, should have been respected. Brennan wants to give her that. Adding to the “Can it get worse?”ness of the case: the victim was five weeks pregnant when she was killed. Hodgins finds particles on the body from a plant that’s commonly grown in gardens and Hodgins, Brennan and Booth head back to the barrio, where they find a community garden. Brennan finds where the body was buried, but she also finds evidence that there was another body there; another body that’s now gone, too.
Booth brings in the gang leader, who denies any knowledge of the shooting, but points out how unusual it is that no one got hit. Booth realizes that the shooting was a ruse for the driver to escape.
In the lab, Zack determines that the victim was killed by a subdermal hematoma and died soon after a blunt head trauma. They find a mark from the weapon, but can’t ID it yet. Hodgins finds evidence of another plant, one that hasn’t been seen in the wild since 1800 and is only in two places nearby: the White House and the private collection of Senator Alan Corman, and Senator Corman happens to be a supporter of oppressive regimes in Central America.
B&B (with Hodgins) head out to Corman’s house. Corman says that because of his relationship with the country, he employs many Salvadorans – all legal aliens. Corman introduces his son, Logan, a landscape architect who sometimes supervises the workers. Logan calls over Hector, the manager, who doesn’t recognize the sketch of the driver. Logan does, though, and says it could be Jose Vargas. Logan defends Jose, saying that he has a wife and a kid and wouldn’t be in a gang. Hodgins, meanwhile, has been poking around the greenery and has found the plant. Brennan spots some soft dirt and digs into it a little and what do you know? Another body. Back at the Jeffersonian, they determine that the second body is a male, who died a year ago. Hodgins finds a military issue bullet lodged in the man’s skull. At the same time, Goodman has determined that the woman was from a village called Milladro de la Pas and Angela has finished the sketch, drawing her with a smile, hopeful.
Booth has gotten Jose’s address from Logan and he and Brennan go to check it out, but find that no one’s there. Brennan sees a picture and recognizes the location; it’s the same place the victims are from. Booth checks the closets and finds a hidden panel where Jose’s wife and child are hiding behind. Booth is trying to intimidate them, threatening to take the child away and deport the woman, but Brennan won’t translate. She explains that the woman has lived with terror and intimidation her whole life. She asks Booth not to ask her to translate, as a favor to her.
In the lab, Brennan and Zack find a shared hereditary marker on both victims – they’re daughter and father. They also realize that bullet had bone growing around it. He didn’t die from being shot. He died from cancer.
Booth isn’t getting any answers from the wife, who has lawyered up. His’s frustrated that Brennan got mushy on him, but it’s okay, he’s agreed to get the gang leader’s sister off some drug charges for the guy to bring Jose in. The way Jose’s brought in? By being thrown from a car with a note: “Special Delivery for Agent Seeley Booth.” B&B visit Jose in the hospital and Jose denies being in a gang. Booth tries intimidation, but Brennan notices something on Jose’s X-ray: the same hereditary marker. She realizes that the bodies are Jose’s sister and father. Booth chalks Jose up as just another stupid gang member, but Brennan pleads with him to give them something, help them do the right thing for his sister, their names at least. Jose speaks: Duarte. Maria and Augustin.
The gang leader, who’s name is Ortez, is back in. He says that Jose was a family guy, but his sister hated him because of his “associations.” Jose wanted to move the bodies because the burial site was threatened by a new development. On his way out, Ortez hits on Brennan, who calls him out for trying to intimidate her. She stands in his way and asks how it feels to face someone who’s not intimidated by him. Ortez goes to lay a hand on her and Booth weakly warns that he shouldn’t but it’s too late. Brennan lays him out. As she and Booth walk away, Booth asks if she feels better. “Yeah, I really do,” she replies.
Angela has heard about Brennan’s run in with Ortez and, as Brennan’s best friend, asks her what the hell she was thinking and advises her that she needs therapy. Brennan tells Angela why this case is getting to her so much; she’s dealt with the intimidation and the fear. On her last visit to El Salvador, identifying death squad victims, she was in a tent by a grave site working on the remains of a 13-year-old girl who had been shot in the head and dumped in a well. A cop showed up. Brennan thought he was a guard at first, but the cop wanted her to stop her work. When she refused, more came. They put a bag over her head and tossed her in a cell for three days. She thought it was longer. They made her think she would die every day, told her they would shoot her and toss her in a well and no one would ever find her. Brennan promised herself that she would get even. Aww, Brennan. I don’t mean this negatively, but you do need therapy, sweetie.
Hodgins has identified the wood particles found in the head wound on Maris. It’s a rare wood used in very expensive furniture, like the kind of furniture that would be found in a senator’s house. B&B take Maria’s picture back to the house and Hector recognizes her as a maid. He says that she just stopped showing up one day. Booth asks if she was involved with the Senator and Hector says no, but she was involved with Logan. B&B question Logan in a room and Brennan notices that the pineapple-shaped posts of the bed could be the murder weapon and sure enough, there’s dried blood and skin on one of them.
In the interrogation room, Logan recalls seeing Maria dancing in the hallway one day and thinking how pretty she was. His lawyer advises him not to answer any questions, but Logan wants to. He says that they started sleeping together just over six months ago, but kept it secret. Brennan reveals that Maria was pregnant and Logan is gutted. The lawyer callously says that they can’t even know it was his, but he’s sure it was.
The Angelator works its magic trying to figure out how their top three suspects (the Senator, Logan and Hector) could have killed Maria, but the angles just aren’t working. With the force that she hit, Brennan realizes that she must have been yanked down from a ladder. She doesn’t know if it was murder, but someone was definitely responsible.
B&B visit Jose in the hospital again and ask him who he was protecting. Jose’s father was undocumented. With a baby on the way, he couldn’t risk reporting his death and getting deported. Same with his sister. Jose joined the gang so that he could get fake papers for her; it was the only way for him to keep his promise to his father to keep her safe. When he failed at that, he just wanted to give them a beautiful place to rest, near a pond. It was all for naught.
At the scene of the crime, B&B have set up a ladder and ask the Senator to try and pull Brennan off. She says that she’s trained in kinesiology, so she can tell if they’re the murderer by the way they pull. The Sentaor pulls and Brennan clears him. Next, they ask Hector, who refuses. He admits that it was an accident. He was just trying to protect his position there, make the problem go away.
An FBI Agent gives Booth a message from the gang task force: Ortez has put a hit out on Brennan.
Brennan and Angela attend a funeral for Maria and her father. Logan is there, as his Jose and his family. Angela tells Brennan she did a good thing by paying for the funeral. Brennan wonders where Booth is. We see that Booth is back in the barrio. He follows Ortez into an alley and corners him, putting a gun in his mouth. He tells Ortez that if anything happens to Brennan, he will kill Ortez and make sure no one ever knows. Back at the funeral, Jose promises to pay Brennan back, but she tells him not to worry about it. Booth runs up and asks if he’s in trouble for missing the funeral and apologizes. Brennan asks if where he was was more important than a funeral. “I thought so at the time,” Booth replies, never revealing what he did.