The episode begins with Hodgins waking up by the sound of his crying baby. His head spins as if he has been drugged. Blood drips on his face. Hodgins looks up and sees a skinned body hanging from a net. He screams and wakes up Angie. They race to the baby's room. Michael is crying but he is fine. They then see that Michael is encircled with bloodied petals. Angela screams. Booth and Brenan are driving and Brenan tells Booth that Hodgins found a hole in the ventilator; this means they were drugged by some gas. Brenan then tells him that Angie thinks that Pelant is back. The two go to Hodgins’ house. Brenan examines the body and tells them that the victim is a male.
Brenan and Booth think that they need proof to prove that this is Pelant’s work. Hodgins tells them that the flowers are from Egypt, where Pelant last was. So, flowers and a dead body; Booth now is sure that it is Pelant. "No teams," Hodgins says. "No one can know about this but us." But Booth disagrees. He says that they will stay within the system. Back at the lab, Brenan examines the body and states that the victim is a Caucasian male. She feels that by skinning the victim, taking out his mandibles, Pelant is trying to send a message; but she is not able to see it. Cam pulls out a pair of tiny, metal fragments in the victim's pelvis and sends them to Hodgins for testing.
Angie is worried that Cam is treating this like any other case. She tells Brenan that Pelant was holding Michael in his hands. Brenan tells her that she should focus on the case and that will keep her distracted. Next, we see that Pelant is taking over a new identity and also creating new IDs. Sweets, tells Booth that Pelant has wiped of his Egyptian identity as well and so now they have no name to start with. Flynn then arrives and asks if the team is looking for Pelant. Sweets, Booth, and Caroline deny it. There can be no leaks of any kind this time. Angie has come up with three reconstructions; due to the lack of mandible, everything becomes sketchy.
Brenan tells Cam that the bones show that the victim had a disease that isn’t domestic; but soldiers are prone to it. Hodgins determines that the metal fragments are shrapnel. Bones and Camille examine the body and theorize that the victim found in Hodgins' house was a member of the Special Forces. Cam tells Hodgins that the hematologist was unable to identify the gas Pelant used to drug them. Cam tells him that there is nothing that they found. Hodgins tells her that he is ready to pay for all the resources; for him nothing is more important than getting Pelant. Later, Flynn brings Booth top secret papers from the Pentagon and an offer to help.
This time, Booth accepts. They ID the body as one of the Special Forces members listed in the files. Booth and Sweets head to the victim's apartment. They infer that the victim was detached and was ready to leave anytime. Sweets, finds a safe. Inside are weapons that indicated the military man had become a mercenary who killed for money. So, Pelant killed a highly trained professional. This sort of a target is not good for Pelant. Sweets states that Pelant is escalating. The question is why? Booth and Flynn head to Serberus, the biggest supplier of mercenaries in the world. They want the details of all the missions Freeman, the victim was on. Molnor, who works for Serberus, tells the pair that the company will not reveal information about the victim or his missions.
He knows about Pelant and he tells them that if Pelant is the man who killed Freeman, then they will find out. Sweets, visits Hodgins and tells him that he needs to have a perspective. He tells him to take a breath. Just then a thought crosses Hodgins’ mind and he goes through some book. Flynn and Booth want a warrant issued against Serberus; but Caroline tells them that she needs something solid for such a warrant to be issued. Sweets meets Cam and tells her that Hodgins is acting maniac and that he needs rest. Can does not want to take Hodgins off the case as she knows that Pelant is scared of Hodgins and that is why he put the body in his house. Pelant too wants Hodgins off the case.
Hodgins tells Angie that he is going to biopsy his lungs as he doubts that there would be some residue of the gas in the tissues; and that could lead them to the source. Angie wants him to biopsy her lung too. Later, Pelant calls Brenan and taunts and also tells her that he is sending her a hint. Later, the mail man finds a severed finger that was supposed to be delivered to Brenan. Hodgins and Angela then biopsy their own lungs and discover a very rare gas. Only two companies provide such a gas, and it turns out that Hodgins' family owns both. Bones examines the severed finger and determines it once belonged to an ape; a particular type that was dissected by an anatomist in the 16th century. So the team compares the skinned victim with one in the anatomist's ancient drawings.
It is a match but the positions are different; so it is difficult to figure out the similarities. Hodgins sends Booth a message saying that a man named Justin Trimple bought the gas. It has to be a paper search and not computer; else Pelant would know. Angela suggests that they should spam Plant which would distract him and that will give them time to search on Trimple. It is low tech but it is also ancient. So she sends hundreds of spam to the Trimples all over and when Pelant blocks the spam, the server that blocks the spam. And that server is inside Serberus. Pelant took the security chip from Freeman and that is how he got inside. So Booth asks for a full SWAT team to raid the Serberus building. Inside, Pelant sees the force assembling outside. He looks worried.
Back at the lab, Bones continues to examine the photo of the victim compared to the photo from the 16th century text book. She notices that some of the muscles on the recent victim have been cut out. So Angela lays the recent photo over the old one and letters peak through the missing parts: M-E-L-Y-C-U. they then find out that it is LYCEUM, it means a school. At Serebus, Booth leads the armed group inside and begins to search. Looking at video feed from the security monitors, he sees Pelant walking through doors and down hallways in six different locations. He cannot be enerywhere; so there has to be another way out. So Booth goes to Molnor and demands to know where the secret exit is located; the one not in the blueprints. Molnor reveals the path and Booth and Flynn follow it.
They spot Pelant and chase him into a small room. Pelant then hits a button on his tablet and a machine gun emerges out of the wall. Flynn is shot and Booth manages to escape. Booth then emerges into a parking garage and sees Pelant driving away. Booth fires and we see blood splatter on the windshield. Later, Flynn is taken away on a stretcher. Booth then tells Sweets that Pelant is wounded. Meanwhile, a code has appeared on the Serberus screens. Booth recognizes them as a military coordinates. Looking at the speed, they deduce that it is a drone; and this type can take out a city black. Angela types in "lyceum" and, suddenly, the team can see where the drone is heading. It is targeting a school in the Middle East; a school for young girls.
The team tries to reroute the drone when Hodgins receives another shocker. His bank accounts are being drained of money, but shutting down the server would mean the team loses contact with the drone. Pelant is forcing him to choose; keep the money or save the girls. He decides to save the girls. With only seconds remaining before impact, Angela makes the drone self destruct. So the girls are saved. Next, Pelant is in a veterinary and the vet is lying dead on the floor. Pelant is sewing his right cheek. The episode ends.