After a right-wing radio host's remains are found in a storm drain, the team narrow the list of suspects after learning about his surprising extracurricular activities, while Agent Aubrey and Brennan both express concern over Booth's state of mind.
A body dumped in a river proves to be a wealthy games designer with a history of manipulating others, leaving the team with no shortage of suspects. Meanwhile, Booth and Brennan begin to consider Christine's future.
A forensic scientist convention becomes complicated when all the attendees want to help determine cause of death for a body found in a stairwell, with the subsequent investigation revealing that Hodgins is a potential suspect. Brennan encounters a rival after making a speech and Wendell returns with an update on his health.
The body of a murdered maid proves complicated when they discover that she was an undocumented immigrant, and Arastoo's preparation for his dissertation coincides with talk of marriage between him and Cam.
Aubrey is troubled by an emotional connection to the case of a murdered hedge-fund trader, and Booth and Brennan face a parental conflict over their contrasting reactions to Christine swearing for the first time.
The team investigate the death of a psychic whose body is found in a tree. They are assisted by Angela's psychic friend, Avalon Harmonia, however some of the team are skeptical regarding her having real psychic powers. Meanwhile, the team remember Sweets, and it would have been his 30th birthday.
An ex-con's body is found in pieces after being blown up in a mine explosion, which leads the team to investigate a bakery which is known for hiring for ex-felons. Meanwhile, Arastoo learns that his brother is dying from cancer, and must decide whether to return to Iran, his birth country from which he fled as a teenager.
The team investigate the death of a professional mini-golfer. Brennan's father, Max, returns, however she becomes suspicious when he says he has to leave town. Meanwhile, Wendell has Hodgins assist him after he accidentally breaks a family heirloom of his girlfriend's.
When the remains of a high-stakes gambler are found in an industrial shredder, Booth goes undercover in an underground poker game, much to the dismay of Brennan, and risks relapsing into his gambling addiction. Meanwhile, Hodgins invents an unbreakable material which keeps glass from breaking when dropped, and Brennan and Booth find out they're expecting a second child. Later, Booth, affected by going undercover, breaks his gambling sobriety and makes a bet.
The death of a TV celebrity chef leads Booth and Brennan to investigate the Royal Diner, a local restaurant the Jeffersonian team frequent for lunch every day. Meanwhile, Hodgins sells his invention for millions, and Cam receives word from Arastoo who is in Iran. Booth buys Brennan a golden necklace with the money he won from the bet, and Brennan becomes skeptical of his behavior when she discovers he left misplaced gambling sobriety chip, an item he always has.
When the remains of a girl are discovered in a ditch, it leads Booth and Brennan to a private high school where they discover she was a victim of bullying. They discover that the girl committed suicide, but made her own death to look like a murder and planted evidence so that the other girls that bullied her would be blamed for her death. Meanwhile, the rest of the Jeffersonian team discover Brennan is pregnant and Daisy ponders whether to start dating again, still reeling from the death of Sweets.
After Brennan reexamines an old case and finds new evidence, she believes Alex Rockwell, a man she and Booth convicted as a serial killer in "The Baker in the Bits" did not actually commit the murders. The team races to prove who the serial killer is as Rockwell will be sentenced to death in 48 hours. Meanwhile, Angela and Hodgins contemplate their future, by possibly moving to Paris, France.
Booth and Cam travel to Tehran, Iran, when they learn Arastoo has been kidnapped by a member of the Iranian parliament to assist in a murder investigation. They must identify the killer for Arastoo to be released. Meanwhile, Brennan learns Booth has been gambling again when his bookie shows up at their home telling her he owes money. When Booth returns from Iran, Brennan confronts him and tells him to leave.
Booth and Aubrey investigate the murder of a woman who was a collector of cookie jars. Meanwhile, Booth, who is no longer living at home with Brennan, begins to attend Gamblers Anonymous hoping to overcome his addiction. Also, Aubrey gets close with Jeffersonian intern, Jessica.
The team investigate the death of a yoga instructor, who was previously a biker gang member. Meanwhile, Booth reaches his 30th day clean and continues to make progress with healing his relationship with Brennan. Angela and Hodgins decide to move to Paris, France, and Hodgins finally learns that Angela's birth name is Pookie Noodlin.
The team investigates the remains of a possible protege of serial killer Christopher Pelant. Angela and Hodgins decide not to move to Paris and stay at the Jeffersonian. Meanwhile, Brennan and Booth move on from their careers at the Jeffersonian and the FBI.