Suspected serial killer Christopher Pelant, the computer genius, clearly hopes to avoid trial by completely discrediting the Jeffersonian team. Playing on their emotions, each in turn is trapped to commit undeniable, often illegal errors, leading to their dismissal as witness or even suspension from duty, as happens with Booth. Given implicit threats to baby Christine and mounting evidence against Bones herself in the murder of her detained mentor Dr. Ethan Sawyer, Max makes a convincing case she would better disappear until the case is cleared.

Months later, Brennan is still on the run from the FBI, after being framed for murder by Christopher Pelant. The remaining team searches for the real killer.

After Hodgins and Angela were drugged and woke up to a bloody corpse hanging in the canopy of their bed and flower petals around their son Michael's crib, they are forced to believe that Pelant is back for revenge against Hodgins. Although Hodgins wants to go after Pelant directly, Booth knows it's best to work within the system and not go against protocol. Meanwhile, as the Jeffersonian team investigates the corpse, they discover the victim was a Special Forces agent working for the world's biggest supplier of mercenaries, and Angela and Hodgins decide to start an investigation without the rest of the Jeffersonian team for the sake of their family.

The team creates a fake murder scene to mimic the work of Chris Pelant, hoping Pelant will contact them about a copycat killer.