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.

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.

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.

The team talk to the deceased teenaged victim as if he is alive. A psychic visits and says the victim called her to help with the case. The boy's spirit affects everyone as they look for his killer.

An archaeologist is found murdered. His lab holds ancient remains of Neanderthals and Homosapiens; these are given to Clark to research. Brennan is jealous that she has to work the current case and not the ancient one.

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 Jeffersonian team investigates the remains of two bodies that were found at the same burial plot: one of a female cancer patient; the other, the doula who was guiding her through her grieving process with the illness. Meanwhile, with a spotlight on the case, Brennan and Booth start discussing their individual choices for after-death arrangements. Also, Daisy Wick returns for her first case after her break-up with Sweets.

When Brennan is shot while working late at the Jeffersonian lab, she is rushed to the hospital in critical condition. While at the hospital, she struggles with visions of her mother that defy her usual logic. Meanwhile all evidence suggests that Brennan's attacker may be linked to the Jeffersonian.

The Jeffersonian team investigates the death of Symchay Conteh, a young man whose remains were found in a barrel at a hazardous waste disposal facility. They discover that the victim was an immigrant from Sierra Leone working numerous part-time jobs in order to make ends meet Meanwhile, as the team gets deeper into the investigation, Cam and Arastoo find it even more difficult to keep their relationship a secret and Brennan and Booth try to decide on a vacation destination.

When the Jeffersonian team investigates the death of a former Marine sergeant whose remains were found burned to a crisp, they discover that she was discharged after a fist fight with another Marine. When Booth and Sweets go to question the other Marine involved in the altercation, they learn that Deanna was obsessed with the idea of the apocalypse, which leads the team to a following of doomsday preppers who become key suspects in her death. Meanwhile, Sweets thinks he has landed his dream apartment but Brennan and Booth are not convinced that he will actually move out.

The Jeffersonian team investigates the murder of a TV producer. Meanwhile, Brennan has trouble accepting the fact that Christine might be an "average" child, when her daughter gets accused of biting another classmate. Then, Hodgins uses all of his tools at the Jeffersonian to chemically recreate Finn's (guest star Luke Kleintank) special hot sauce.

The Jeffersonian team investigates the murder of Jack Spindler, a successful employee at a brokerage firm by day, but a stripper by night. When the team learns how Spindler's moonlighting affected his personal life, they start to question the people closest to him, including his stripper friend, Storm. Meanwhile, Booth's mother shows up after a 24-year absence in his life and makes a special request of him.

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.