A human spinal column was deposited at night at the Lincoln monument with a message taunting to find the rest. Its vertebrates were reassembled, forming a code Hodgins gets obsessed with solving. The blood on it stems from 5 FBI agents, who donated it at the Red Cross. Sweets and his profile help Booth identify suspects, notably brilliant hacker Christopher Pelant and the omnipresent newspaper reporter Ezra Krane. Another murder follows and a highly original diversion crime. Bones meanwhile accepts to stay home and seriously considers Booth's ideas for a new home.

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.

When evil tech genius Christopher Pelant returns to toy with the Jeffersonian team in their newest investigation, they discover that the string of murders that have been occurring are tied to FBI agents close to Booth. Meanwhile, as the investigation unfolds, Sweets realizes that the evidence seems all too familiar to him and Brennan starts evaluating her relationship with Booth when signs begin to point to him as a potential target of Pelant's.

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

The Jeffersonian team investigates the death of Lana Brewster, a girl whose remains are delivered to Brennan and Booth's home by someone who believes her death 18 years ago was no accident. When the team discovers that Lana was murdered and her death was covered up, people from her past become key suspects, including an ex-boyfriend with whom Hodgins was friends. Meanwhile, Brennan starts having dreams again about evil tech genius Pelant, and about a potentially more heinous killer, whom she realizes could be involved with Lana's death.

In 1950s Hollywood, Brennan is a LAPD detective faced with sexism on the force, and Booth is a notorious jewel thief - who is framed for murder.

As the team investigates a murder, evidence found in the crime scene reminds them of an old enemy. Elsewhere, Angela worries about Hodgins' and her decision, while Booth and Brennan consider a life without the Jeffersonian.