Hodgins (T.J. Thyne
) is awoken by the sound of his crying baby. However, the room swims as if he is drugged. Blood drips on his face. Hodgins looks up ... and sees what appears to be a skinned body hanging from a net. They race to the baby's room to find the child encircled in bloody flower petals. Angela (Michaela Conlin
Everybody safe, but scared. "Angela thinks Pelant is back," Bones (Emily Deschanel
) tells Booth (David Boreanaz
). The two go to Hodgins and Angela's home -- and discover the flowers are from Egypt, where Pelant last was. "No teams," Hodgins says. "No one can know about this but us." Booth disagrees. "We stay within the system," the FBI guy decides. Back at the lab, Camille (Tamara Taylor
) discovers a pair of tiny, metal fragments in the victim's body and sends them to Hodgins for testing.
Sweets (John Francis Daley
), meanwhile, discovers Pelant (Andrew Leeds
) has wiped out his identity -- again -- so the team doesn't even have an official name with which to start. Flynn (Reed Diamond
) then enters and asks if the team is looking for Pelant. Sweets, Booth, and Caroline (Patricia Belcher
) deny it. There can be no leaks this time.
Hodgins determines the metal fragments are shrapnel. Bones and Camille examine the body and theorize the victim found in Hodgins' house was a member of the special forces. Later, Flynn brings Booth top secret papers from the Pentagon and an offer to help. 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 and find a safe. Inside are weapons indicating the military man had become a mercenary for hire. "A target like this is a big risk for Pelant," Sweets notes. "He's escalating."
Booth and Flynn head to Serberus, the biggest supplier of mercenaries in the world. Molnor, who works for Serberus, tells the pair the company will not reveal its proprietary information about the victim or his missions. Hodgins, in the meantime, is acting manic. Sweets takes notices and brings his concerns to Camille, who refuses to take Hodgins off the case. "Pelant is scared of Jack Hodgins," she notes. "He wants him off the case." Later, Pelant calls Bones to taunt her -- and to also promise a forthcoming "hint." Sure enough, a young man in the mail room discovers a severed finger in a delivery for Bones.
Hodgins and Angela then biopsy their own lungs -- a painful procedure -- and discover a very rare gas. Only two companies provide such a gas. It turns out Hodgins' family owns both. "I'm going to take care of this myself," he says. Bones examines the severed finger and determines it once belonged to an ape -- a particular kind once studied by a 16th century anatomist. The team compares the skinned victim with one in the anatomist's ancient drawings. It's a match. "But what does it mean?" Camille asks.
Hodgins discovers a man calling himself Trimple bought the gas knocking out Hodgins and Angela in their home. But how to find this Trimple? Angela suggests "spamming him," a low tech approach that might just work because it's ancient. Basically, she sends out hundreds of spam email to Trimple's all over. When Pelant blocks the sender, the server from which he is working is revealed. And that server is inside Serebus. Pelant has reprogrammed the victim's keycard to get inside the security firm.
Booth asks for a full SWAT team to raid the Serberus building. Inside, Pelant sees the heavily armed 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 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. Or "lyceum," a school.
At Serberus, 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. The hacker/killed is covering his tracks. Booth goes to Molnor and demands to know where the secret exit is located -- the one not in the blueprints. Molnor reveals the path. Booth and Flynn follow it. They spot Pelant and give chase into a small room. Running, Pelant hits a button on his tablet and, inside the small room, a panel drops and a machine gun appears. It riddles Flynn with bullets as Booth narrowly escapes. Booth then emerges into a parking garage to see Pelant driving away. Booth fires. Blood splatters, but the car doesn't stop.
Moments later, Flynn is taken away on a stretcher. Booth then tells Sweets about wounding Pelant. Meanwhile, a code has appeared on the Serberus screens. Booth recognizes them as a military coordinates. Turns out Pelant has programmed a drone carrying enough explosives to take out a city black. Angela types in "lyceum". 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 works furiously to reroute the drone when Hodgins makes another shocking discovery. 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 me to choose: keep our money or save the girls," Hodgins explains. He quickly makes his decision. "Save the girls." With only seconds remaining before impact, Angela makes the drone self destruct.
The girls and the team is saved -- for now. Pelant is gone once again. Flynn, on the other hand, might not live. Pelant has been shot, though nobody knows the extent of the damage. The episode ends with Pelant inside a veterinary clinic. The doctor is dead. As the dogs bark, Pelant sews up his own face.