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.
Body parts float up in a toilet. The team determine the deceased was a prisoner. Booth wants Brennan to take it easy since she is near her due date. Dr Brennan & Booth go to the prison to find the killer. Afterwards, Brennan gives birth.
Finn Abernathy's Dixie country experience proves as useful as his IQ in figuring out a female corpse smeared over half a mile of interstate road by Alan Bates's truck. The victim, farmer's wife Barb, was a fanatic even by the standards of her coupon addicts club, all of whom bicker and bother Chad Fergus's supermarket, where a cashier was filmed beating Barb. Her husband Dale Berquist spend lonely nights dining with other women. Finn proves a perfect gentleman when Michelle shows interest in dating him, yet now Camille re-questions his past.
Hodgins has a hard time identifying the blue substance which killed animals scavenging on a scalped corpse, painstakingly identified as a capricious star hairdresser. Possible motives include a bizarre cult, salon rivalry and a form of organ theft. Sweets counsels Booth how to handle Bones' apparent postnatal self-image-issue.
Metal hardware deliverer Tony Cole was fatally stabbed in a puzzling way. Booth is more preoccupied with his son Parker, finally back from England, and how to fit him in the family with Bones and baby sister Christine, and Sweets is through with counseling under false pretenses. Hodgins uses the case to prove his expensive 'pet' equipment is all useful. Tony had a bitter company rival, Karl Singler, and picked a fight with his beloved boy Danny's karate sensei, Hunter Sherman, over a fight with sprout Blake Sherman.
A West Virginia truffle hunter's hog stumbles upon a corpse in the woods. The killing may fit in over a century of vicious, vivid feud between the neighboring Babcock and Mobley families, which a lawyer in the family had until recently converted into endless litigation. Natural resources and forbidden love may also prove crucial. Sweets gets to interrogate on his own while Booth is preoccupied with stopping Bones from chasing all baby-caregivers, even her own father.
The corpse of the boss of the Hollywood studio where extravagant British director Joco Kent is filming "Bone of Contention", an action movie based of a book by Bones, is dropped in a clumsy attempt to cover up a bizarre stabbing. He had enemies and his demise opens opportunities. While investigating, Booth is offered a lucrative security job there. The Jeffersonian team is jealous of scientific consultant Dr. Douglas Filmore, but they all get to prove their worth.
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.
A burned body is found. The victim is a divorce lawyer who had a lot of disgruntled clients. With Brennan back home, she and Booth have to adjust to living together. They have various disagreements about the new routines at home.
A man dies in a car explosion. After identifying the man, Booth and Brennan find he is still alive. Turns out, the two guys are twins who did not know of the other. Both men are browbeaten by their wives, one of which wanted her husband dead.
The team identify a woman's eviscerated body as a co-owner of a natural applesauce store. There is a symmetry to her incisions. Sweets has been living in his office since the breakup with Daisy so Booth invites him to stay with him and Bones.
Brennan, intrigued by Phil Jackson's management style, pulls all her interns together as a team for a project worthy of the basketball coach's philosophy. She charges them with identifying remains that have been determined unidentifiable. For the team, however, it turns out that naming the bodies may be the easiest part of their task when one of them is from 9/11 and they must decide if he is a victim or perpetrator.
The Jeffersonian team investigates the death of a crime scene cleanup expert whose remains are found mysteriously sealed in an impenetrable pod that washed up on the beach. Meanwhile, Angela and Hodgins learn that Cam is involved in a secret romance.
An artist gluing his artwork on a billboard slips and falls with his glue on top of a corpse. The team has to separate the artist from the bones. Angela realizes the artist is a famous street painter. Bones takes up comedy to find suspects.