Booth has Cam rather than Brennan accompany him to a crime scene, where a stabbed, kneecapped, naked corpse is found. There's a jade gemstone inside the stab wound. At the lab, it's found that the kneecaps were surgically removed.
That night, Brennan is visited at home by Amy Hollister - her brother Russ' girlfriend. Amy's younger daughter, Haley, who Russ was helping to raise, has Cystic Fibrosis. It's getting worse, and Haley's been asking for Russ. Brennan says she has no idea where Russ is and that Amy should ask Max. She also refers Amy to the top Cystic Fibrosis specialist in the country, who is a friend of hers. As they speak, Brennan notices a package in her pile of unopened mail has begun to... bleed. She ushers Amy out, and then opens the package - to find that the murderer has mailed her the missing kneecaps.
The envelope was mailed from the D.C. area. The patellas are unusually worn. The victim must have done a lot of kneeling. The cloth the kneecaps were wrapped in bears a strangely familiar seal. And Zack finds the murder weapon is identical to that used by the Gormongon/Widow's Son killer. The seal is Masonic. Dr. Sweets arrives because Booth and Brennan missed their session; he gets caught up in the investigation, and thinks the kneecaps might fit the Widow's Son silver skeleton. Angela thinks there's something wrong with the tapestry behind the skeleton.
Dental records show the victim is Father Douglas Cooper who is Vicar General to the Archbishop of Washington, D.C. Booth and Brennan interview the Archbishop, who says Doug had been working on a book about early Christianity and its ties to paganism.
Zack and Cam find the victim was hung by his arms for a long time, possibly in the position of the Widow's Son sculpture. Angela finds the figure on the tapestry is Barabbas. The Gormongons, who were against Masonic secret societies, believed they were founded by Barabbas. He is a symbol of all that's backwards, upside-down and inside-out.
Inverting the numbers on the tapestry and plotting them on a map of Washington - a city that was laid out according to Masonic symbols - shows the location of the Widow's Son vault and the murder scenes as well as an old mansion that's now a nursing home and a mausoleum. Booth and Hodgins investigate the mausoleum, inscribed Pater Mortuus - "Dead Father." Inside is another Widow's Son sculpture - this one entirely made of bone.
Brennan visits Amy and Haley at the hospital. Amy says she wasn't allowed to visit Max because she's not a relative. She begs Brennan to visit him and have him get a message to Russ.
Zack finds at least 18 different victims in the new skeleton, all with indications of cannibalism. And the bones are over 50 years old. Is Gormongon an old man? The teeth marks don't match the teeth marks on the other skeleton or on Doug's body. Doug's body contains dirt from a region of Turkey which legend says is the original site of the Garden of Eden.
Brennan visits Max, who says Russ sends money every month. Brennan tells Max to just tell Russ Haley's very sick and asking for him, and make up his own mind what to do.
Angela finds the tapestry contains symbols of several Masonic archetypes: The Architect, The Martyr, The Orator, The Musician, The Bishop, The Corruptor, The Scientist, The Hermit, The Teacher and The Judge. Booth realizes that Gavin was the Musician and Doug was the Bishop. Gormongon is going in order, counterclockwise. The next is "The Corruptor."
Booth had given the case file to Sweets, much to Brennan's consternation. Sweets says that a "corruptor" would be a heretic, or somebody who upsets the natural order and a pretender to a throne. Sweets thinks there's a duo of cannibals - a Master and an Apprentice. When the Master retires, the Apprentice becomes the Master and starts his own project. Both victims are widow's sons. Booth says they already found the Apprentice and he killed himself. Sweets thinks the Master had access to at-risk children for his recruiting. Turns out Gavin and Doug went on the same trip to Turkey last year, and it was arranged by lobbyist Ray Porter. A lobbyist could be a "Corruptor."
Booth and Brennan interview Porter, who is a member of the Knights of Columbus, and whose father died when he was young. They try to warn him he's in danger, but he thinks it's some sort of trick having to do with an FBI investigation into influence peddling on his part, and throws them out.
Russ Brennan shows up at the Jeffersonian. Booth immediately places him under arrest. Russ is shocked; Max had said that Brennan had said Booth wouldn't arrest him. Brennan denies it, but Russ doesn't believe her. He begs to see Haley. Booth isn't going to oblige, but Brennan prevails upon him. Russ gets to see Haley, and Booth lets him have 15 minutes with her before pretending to "find" and arrest him there.
Brennan confronts Max about his lie. He says he was just trying not to get her in trouble with Booth. Brennan tells him he's making it so she and Russ can't trust each other.
Zack discovers a camera the skeleton's eye. Gormongon's been watching them all along. Booth and Brennan decide to pretend they're transferring the skeleton so maybe Gormongon will try to grab it. They stage a scene in front of the skeleton, discussing the "transfer," and Brennan is none too convincing.
As they drive a taxi, undercover, a figure on a motorcycle, in a reflective black helmet, drives by. The person drops a backpack on the road in front of the taxi. Booth realizes it's a bomb and turns away just in time, though the taxi is still flipped over. Brennan is injured. A wound in her shoulder reveals a human tooth meaning that the bomb used teeth for shrapnel. Gormongon knew it was a set-up and tried to kill them. They realize that he knows they are aware of his next target.
Booth rushes to Ray Porter's home to find him gagged and trussed up naked, in the position of the Widow's Son skeletons. Porter says he had a knife. Booth spots the man from the motorcycle and pursues him, but he uses a child as a shield and gets away while Booth tries to save the child from drowning in a swimming pool.
Brennan visits Russ in jail and says she's come to realize there are levels of bad guy, and Russ isn't even on the first level. But she doesn't believe Russ that he knows nothing about their dad's murder case. However, the siblings begin to come to some sort of rapprochement. Brennan goes to AUSA Caroline Julian and pleads for Russ to be set free, telling her that Russ actually came back of his own free will and Booth didn't "catch" him. Caroline refuses, but allows her to speak at the parole hearing.
Zack finds the teeth in the bomb are Gormongon's, and they were all pulled out with pliers. Sweets says the cannibal was symbolically biting them, though Brennan takes issue with the "symbolic" part. Sweets theorizes the skeleton is a "whacko" attempt to recreate Adam. As in Adam and Eve.
Zack finds the number 1026 on a rib; they check the Gormongon Vault safety deposit box 1026. Inside is a key with a bar code; it's an old key from the 1970s to room 1026 at the Municipal Department of Social Services. In the 1970s, the room was used for foster care services - a great place from which to recruit disturbed boys. The man who worked there, Arthur Graves, now lives in the nursing home that used to be a mansion. They visit him; he has Alzheimer's and isn't lucid. They want to take a dental record, but he has no teeth - they were pulled before he got there.
At Russ' parole hearing, Booth remains silent but the Archbishop and Dr. Sweets have given statements of faith in Russ, which Brennan realizes Booth has arranged. The judge sentences him to 30 days in county jail, adds 18 months to Russ' parole and compels him to wear an electronic monitor. Caroline Julian's miffed at Booth, but Amy's grateful. Booth warns Russ he'd better not run again.
That night, Ray Porter, upon arriving home, finds a 15-year-old boy in his closet with a ceremonial dagger and a crazed smile. The boy attacks.