Booth lies dying as Brennan tends to him. The image fades from Brennan's memory and she's back in the lab, working on a skeleton. The squints file in, dressed in black, ready to attend Booth's funeral. Brennan tells the solemn group she won't be attending. She doesn't see the significance in gathering around a hole in the ground. Angela pulls Brennan aside. She needs Brennan, her best friend, to be at Booth's funeral with her if she's going to get through this tough time. Brennan agrees to go, for Angela.
At Arlington National Cemetery, the group is gathered around Booth's casket as Caroline Julian says a few words. Its clear Brennan is uncomfortable; she would have gladly taken the bullet meant for her. As the Honor Guard moves into place, a mysterious looking man watches from a distance. The seven man guard readies to fire as the mysterious man makes his way toward Booth's grave. The man pulls, from his jacket, a single white rose and is quickly taken down by Booth, dressed as an Honor Guard who knocks the man to the ground. The two men fight, knocking over the casket and the mannequin inside it. The funeral-goers watch as Booth struggles with the man. As the mysterious man goes for a gun, Brennan knocks him in the head with a mannequin arm. The mysterious man lies unconscious on the ground as Booth hops up to thank his partner. Brennan greets him with a punch in the face, before storming off.
Later in the lab, Booth tries to explain faking his death to Brennan. It was the only thing the FBI could do to catch the mysterious guy at the funeral. The wanted man had gone underground, vowing to one day dance on Booth's grave. Brennan doesn't want to hear it. She knew Booth's funeral was going to be "a complete waste of time." And she assures him she won't be at his next one. Booth thought Brennan knew he wasn't dead, he told the FBI to notify her; it wasn't his fault. Sweets points out that the real reason Brennan is upset is because the funeral made her face emotions she'd have rather kept hidden. Brennan feels as if she's been manipulated but the conversation quickly turns as Zack hands Brennan a package with her name on it. She opens it to find a jawbone with two silver screws drilled into it. Brennan indentifies teeth marks on the mandible. The silver and the gnaw marks both point to the serial killer, Gormogon.
In the lab, Brennan, Cam, Hodgins, Angela and Zack watch as Sweets is interviewed about the Gormogon case on TV. Booth is on the roped-off platform deciding what to do. The platform is now a crime scene but they need the platform to investigate the crime. Cam makes the decision for Booth and the squints go to the platform, ready to get to work on identifying the victim. Brennan, Cam, Hodgins and Zack huddle around the jawbone. To find the identity, Cam says she'll search the tooth sockets for DNA. And since the bone appears to have been boiled, Hodgins is going to try and pull some minerals traces from the water while Zack checks out the gnaw marks.Back at his apartment, Booth relaxes in his bathtub with a beer hat, a cigar, a comic book and some loud music. As he slurps his beer, Brennan barges in. She's still upset that he didn't tell her he was alive. Booth tells her how he was just following protocol but Brennan feels as if her partner has no concern for her. An enraged Booth stands to make his point, citing the fact that he did take a bullet for her. After an awkward beat, nude Booth sinks back into the tub. Brennan still wants an explanation as to why she wasn't told. Booth promises to find out why his bosses neglected to inform her. Brennan leaves and Booth goes back to his beer and comic book.
In the lab, Zack and Hodgins have discovered the markings on the jawbone are from a pair of dentures, but not just normal dentures, homemade ones. Booth calls and wants to know if they've identified the victim. Cam tells him it's the Lobbyist. Knowing how much the fake teeth can help, Hodgins and Zack go off to recreate the dentures.
Later in the Gormogon Vault, Booth, Brennan and Sweets look over the Silver Skeleton. Sweets thinks they should add the jawbone to the skeleton; it's what Gormogon wants, it's why he included the silver screws. Booth wonders how the killer would even now if they added the bone. Sweets comments on how it's Gormogons obsession; he has to have some way of finding out. Brennan, once again, brings up Booth's lack of concern for her, and they discuss Brennan's surprise visit to Booth's apartment. Sweets thinks the way Booth chooses to relax is odd. Booth tries to explain the beer hat and comic books.
Back in the Ookey room, Hodgins and Zack are hard at work recreating the dentures. Zack is behind a protective shield wearing preventative gloves as he readies to pour the heated monomer into the denture mold. Hodgins goes to retrieve the mold as Zack begins to pour the monomer into the melting thermoplastic. The crucible explodes and the glass shatters. Smoke fills the room and the alarm sounds as Booth and Brennan rush in. Hodgins lies dazed on the floor, but is okay. Zack is not though. He's in shock as his hands have been shredded in the explosion.
Later in a hospital room, Booth and Brennan sit with the injured Zack. Booth tries to assure him that everything is going to be alright but Zack knows his hands will never be fully functional again. Hodgins, Angela and Cam enter. The two victims of the blast wonder what could have ignited it. Everything, all the chemicals, matched up. The group files out and Angela stays to comfort her injured friend.
Later in the lab, Hodgins works on his analysis of the explosive residue. Sweets says that the FBI is investigating the matter, in fact Agent Howie Madison sits nearby conducting his own analysis. Hodgins isn't taking any chances, as he knows there is a possibility of a secret society's involvement, citing how some secret societies have far reaching arms. Agent Madison interrupts them with an ID on the cause of the explosion. It's a chemical called tricyclic acetone peroxide and it had an explosive reaction when it was mixed with the molten thermoplastic. The monomer containers had been switched.
Booth drags Sweets into Brennan's office, where the angry agent tells his partner the FBI sent his list of people to inform of his fake death to Dr. Sweets. Sweets chose not to tell Brennan that Booth was still alive. Sweets explains that he knew Brennan could handle Booth's death and since it was a case of national security, the fewer people who knew the better. Brennan accepts his answer. But she's still mad at Booth because he should have told her personally. Cam interrupts. There's something in the Gormogon vault they need to check out.As Booth, Brennan, Cam and Sweets make their way to the vault, Brennan pulls Sweets aside. She knows what he was up to; Sweets was experimenting with the partners for his own research. She warns Sweets to cut it out, because if Booth was to find out, he'd beat Sweets up.
Moments later, the four of them meet up with Hodgins in the vault. The silver skeleton is missing. Hodgins knows that the loading dock door was left unlocked. There were no security guards around as they were all tending to the explosion. Cam remarks how all the security cameras failed after the explosion and didn't turn back on until fifteen minutes later. Cam thinks the explosion was a diversion for Gormogon to come in and steal the skeleton. They now know that either Gormogon or his apprentice work in the lab and Booth calls to have a full forensic team sent in.
Later in the vault, the FBI forensic team investigates the burglary. Caroline Julian instructs Cam to stop bothering the techs and to let them do their job. Caroline tells Cam she shouldn't even be around; she's a suspect just like everybody else with full security clearance and complete access to the lab.
Booth and Brennan are in the diner having coffee and discussing the situation. Sweets enters with a profile of someone he feels could possibly be Gormogon. He thinks Hodgins is the killer. Hodgins' clinical paranoia and felling of superiority lead Sweets to his hypothesis. As Brennan sticks up for her friend and co-worker, Booth can't help but agree with Sweets. Hodgins does know all about secret societies and he is the one who figured out the patterns which led them to the vault. Brennan says Hodgins was just doing his job. Sweets notes how Hodgins had access to all the chemicals Zack was using. But Brennan did too, and she mentions this as she asks Sweets why she isn't a suspect. He tells her, because of her emotional connection to Booth and a reverence for life, she can be discounted as the serial killer. Brennan has had enough of the conversation and leaves. Booth follows her out.Back in her office, Brennan tells Cam that Sweets suspects Hodgins. Cam thinks blaming Hodgins would take the heat off of Sweets. Cam explains to Booth and Brennan how Sweets could be Gormogon: Sweets showed up right after they found the Gormogon vault, he had full security clearance to the Jeffersonian and he's the only one unaccounted for after the explosion. And even though they have no evidence on Sweets, Cam claims she can smell it on him.
Hodgins shows up in Cam's lab wanting to know who the suspect is. But Cam can't tell him anything. Hodgins tells her he's found something. The jawbone was boiled in tap water with a high concentration of lead in it. By matching the lead level in the water with the levels of surrounding neighborhoods water supplies, Hodgins was able to find, what is most likely, the killer's neighborhood. It's Hodgins neighborhood. Knowing he's considered a suspect, Hodgins states how he could have left that part out if he wanted to, but Cam knows that if someone else discovered this fact it would have only raised suspicions pointing to him. Hodgins leaves.
In the diner, Booth and Brennan meet up with Sweets. They interrogate him as to his whereabouts after the explosion. He claims to have left to call 911 and after that he led the EMT's to the area of the explosion. He also states how he went down to the vault and stole the silver skeleton. Booth and Brennan miss the sarcasm and look at that statement as a confession. Booth wants to lock Sweets up while he checks out his story. Sweets thinks Booth is projecting his aggression toward Gormogon onto him and if he wants to arrest him, he isn't going to make it easy.
In Zack's hospital room, Angela is joined by Hodgins. Zack wakes and tells the two about his dream; a flaming skeleton held his throbbing hands. He tells Hodgins that nobody could have switched the chemicals and as he tries to explain, Hodgins hits a button administering a painkiller drip to Zack. Zack passes out before he can finish explaining.
On her way out for the night, Cam stops by Brennan's office to find Brennan still at work. Brennan's found something on the jawbone. It's been treated with ultraviolet light; standard procedure for Jeffersonian employees before storing a bone. Brennan thinks Gormogon and his apprentice have been storing their skeletons amongst the Jeffersonian skeletons. Cam wonders how they are going to sift through the thousands of museum bones.
Brennan and Angela speak with a group of Grad students in Limbo, the Jeffersonian storage area for human remains. Caroline Julian watches on from the sidelines. The Grad students will be in charge of making sure the bones in the bins correspond with the label on the bins.
Later in Limbo, the grad students are hard at work as Brennan speaks with Caroline. A grad student interrupts with his findings. An extra femur has been discovered in one box, and extra fibula in another; both boiled. Both bones belonged to a man in his mid-forties to early-fifties. Another grad student has found an extra manubrium, an ulna and a humerus. The students have laid out their findings anatomically.
Caroline, Brennan and the grad student head over to the laid-out remains and Brennan confirms the partial skeleton to be of a man 45 to 50 years old. He was around 5'8. Brennan wants Cam to run a DNA test against all Gormogon's victims. Seeing as the skull is missing its mandible, Brennan believes it is a match for the jawbone she received in the mail. Another Grad student calls Brennan over with his discovery. He has a table full of skulls, all of which are missing their canine teeth. Caroline orders the security footage of the room for the past six months, the area isn't under surveillance. Brennan hurries off, saying she needs to reexamine the jawbone Zack had been working on before the explosion.
Later on the platform, Caroline and Cam huddle over the computer. It's confirmed that the DNA is a match for the missing lobbyist. Cam picks up a tray of gnawed-on bones and heads off to find Brennan.
Cam has the tray of bones before Brennan. She thinks they'll match the denture markings that Zack found. Brennan's busy reexamining the mandible. The marks Zack claimed came from artificial dentures, in fact did not. Brennan takes off with the jaw.
Booth enters Brennan's office to find her behind the computer. Brennan tells Booth that Zack knew the dentures weren't artificial; any first year student would know they weren't fake. She knows that the dentures were made by real teeth, all canine's. She goes on to explain how canines represent the wolf, which appears in the Gormogon tapestry. Brennan tells Booth that certain sects look at the wolf as a symbol of freedom. Booth wants Brennan to get to the point. She tells him: Zack made the dentures from the teeth in Limbo. Booth realizes the Zack had total access to the lab, he arranged for the explosion. Zack's the killer.
Cam is in Zack's hospital room reading a technical magazine to him when Booth and Brennan enter. Cam is able to gather by their moods what is about to take place. She leaves the room. Zack knows they looked at the mandible. He was going to sneak out of the hospital to destroy the evidence but his friends never left his side.
The explosion was bigger than Zack anticipated because Hodgins argued with him, eating time and allowing the thermoplastic to reach its boiling point. The result was an explosion three times the magnitude of his initial calculation. He knew how badly he was going to be injured but had to make sure Hodgins was far enough away to avoid injury.
Zack refers to Gormogon as The Master and he refuses to give Booth his real name. Zack says The Master's logic is irrefutable and if Booth and Brennan only knew what Zack knew, they'd be proud of him. Zack believes the human experience as a whole is greater than a single person's life. It's why he helped The Master and the secret society. But yet, as Brennan points out, Zack threw his entire belief system out the window in order to make sure Hodgins was safe. Zack begins to cry and he explains it all to Brennan. The Master first approached Zack three months ago and as he continues Booth interrupts, he needs to know who The Master is. Zack mentions how The Master took him to his house, but blindfolded. By remembering the turns and calculating the speed, Zack was able to locate the house on a map. He gives Booth the address.As Zack's narrators the directions, Booth and a team of FBI agents swarm the house. They go around back to the blue door Zack mentions. He tells them of the key they'll find hidden above it. Booth finds the key and opens the door. He leads the team of gun drawn agents down the hall. They bust through a door to find Gormogon seated at a table eating meat. Gormogon smiles, revealing his canine dentures. He raises and throws a dagger, hitting an agent. Booth fires his shotgun sending Gormogon through the air. The cannibal's lifeless body hits the floor and it's finally over.
In the hospital, Caroline speaks with Zack as Brennan, Cam, Angela and Hodgins wait behind the glass doors. Booth and Sweets enter and tell the group they got Gormogon. Brennan asks who he was and Sweets tells her; he was nobody, an invisible man angry at history for refusing to recognize him. Caroline leaves Zack's room and tells the group Zack never ate anybody, but he did confess to killing the Lobbyist. Caroline explains that Gormogon prayed on weak personalities, he took advantage of Zack. Caroline thinks she can cut a deal; if Zack pleads guilty she could find him non compos mentis, he'll be taken to a psychiatric facility instead of prison. Sweets reluctantly agrees to go along with it. From behind the glass doors, the group gets one last look at their friend.
Later in the lab, Booth, Brennan, Cam, Sweets, Hodgins and Angela sit around. They all talk about what they could have done to prevent Zack from becoming a killer. Cam is having a hard time feeling bad for Zack though. Zack killed somebody and Cam believes he deserves to be locked up for the rest of his life. Sweets mentions that Cam's strong reaction is just her way of dealing with grief. The focus turns to a box Hodgins has gathered. It's some of Zack's favorite things.
The group goes through the contents; a trophy labeled "king of the lab" from Cam, a pocket-size karma sutra from Hodgins, a harmonica from Booth and a caricature drawing from Angela. Sweets notices how Zack's favorite things were items given to them by his friends. Brennan realizes she never gave him anything though, and she leaves. And away from the group, Booth catches up with her. They take a seat on the stairs and Booth reads to her. A letter taken from Zack's box of things. It's a letter of acceptance to become Brennan's intern. Booth tells her she gave Zack something great. Brennan rests her heavy head on her partners shoulder.