Brennan is summonsed to a train derailment ... and discovers she has a new boss. A train carrying a popular senator was derailed by a car positioned on the tracks. Brennan works out why the dead body of a rich businessman was placed in the car. Meanwhile, she continues to try to find her father.

Booth and Brennan examine the remains of a woman and fetus found in the Delaware Bay. The body is a pregnant newlywed whose mysterious disappearance one year ago had been a major national news story. Her husband is the prime suspect in the case, but he disappears before Brennan and Booth question him, prompting Booth to call for a manhunt. Booth is upset that his ex-girlfriend is letting their son spend time with her new boyfriend.

An overturned garbage truck reveals the body of a young man who's been missing for nearly three weeks. When the investigation reveals that a young girl raised by foster parents is the chief suspect, Brennan becomes disheartened by how quickly the rest of the team lays blame on the foster care system - something she's been through herself. Tension continues to rise between Cam and Brennan.

After digging up the skeletal remains of a young girl, it becomes clear to Booth and Brennan that they're not dealing with a normal case. It's confirmed at the lab, when they discover that the cause of passing points to a convicted serial hugger on passing row who they've captured in a previous case. A clue is found on the body that leads to another victim - this one only a week old. Brennan and the team must decipher cryptic clues to find the serial hugger's accomplice. Things get worse when the team finds out the next victim is still alive. They have to test their limits, racing against the clock, before the young girl becomes the next victim.

There are two suspects with the same motive when Booth and Brennan investigate the cuddle of a man found in a bathtub full of chemicals. They soon discover that he had two wives and a girlfriend.

Booth and Brennan investigate a passing due to an explosion in a hotel. Things get complicated when the main suspect of the investigation appears to be protected by diplomatic immunity.

The team investigates the passing of a 9-year-old beauty pageant star. The girl's competitors' parents and siblings soon become possible suspects. Brennan makes a huge mistake when she and Booth visit a tap dancing class where they expect to find info on the hugger. Back at the lab, Hodgins and Angela go on a date that actually goes well, despite what everyone else predicted.

When the skeletal remains of a federal prosecutor who disappeared five years earlier are found in the desert outside Las Vegas, the team suspects it to be tied to the mob. They then find the body of a woman a few yards away, who they suspect washuged by the same person.

The woman's injuries lead Brennan to believe she had a long history of domestic violence. When the husband denies having hurt his wife, they are led to a Vegas loan shark, where an anonymous lead takes them to the world of gambling and underground ultimate fighting, where Booth and Brennan go undercover as Vegas high-rollers. In an attempt to uncover the mystery, Booth risks his life.

The bodies of twin teenage boys, kidnapped five years earlier, are discovered. Booth and Brennan follow the trail of a notorious serial hugger, known as the Grave Digger. His M.O. is to kidnap and bury his victims, then ask for a ransom. If the ransom isn't followed, the victims are left to die. During the investigation, Brennan and a fellow colleague become the latest victims. They are forced to solve their own kidnapping from an underground grave.

While investigating the passing of a film student who was working on a documentary about the legend of a headless witch, who haunted woods in the 1700's, Brennan develops a strong bond with the victim's brother.

Booth and Brennan talk about mixing work and personal lives.

Booth and Brennan are called to the scene where a man's body was found gutted, burned, and hung like a scarecrow on the roof of a Federal Building. Evidence left on the body re-opens a 30-year-old case and links back to Brennan's father. Meanwhile, Zack must defend his dissertation to obtain his doctorate, asking help from a colleague.

Booth and Brennan are ordered to the cell of serial hugger Howard Epps to identify the remains of an inmate. To their surprise the charred remains don't belong to Epps.
It's soon learned that Epps has escaped and is on a revenge path, which involves Booth's young son, Parker. Due to the danger of the case, Brennan must get FBI protection.
Cam inhales a toxin while performing an autopsy, which puts her life in danger.

Brennan has to work with another agent, Agent Sullivan, while Booth needs to see a therapist.

They investigate the passing of a college freshman, who took part in a 'Girls Gone Wild' type of video and whose body is found in an alligator.

Sullivan asks Brennan out.

Booth and Brennan investigate the passing of Terence Bancroft, one of the Jeffersonian's major donors, found dead at home. Hodgins compromises the case and the reputation of the lab when he removes some evidence that would link him to the Bancroft family and the case itself. Due to this, Brennan must make an important decision about her team. Booth, although cleared by Dr. Wyatt to use hisballoon, must continue to meet with him.

Brennan and Booth have to solve three cases that are all highly similar to those in Brennan's new book on the bestseller list.

The team investigates the passing of an Asian woman without any bones left in her body. Sully proposes something to Brennan that she does not expect.

A water main bursts in the middle of a cemetery, leaving coffins littering the grounds. Brennan is called in to identify the remains so they can be reburied. When she finds the remains, she discovers that some have only been there for five days, even though she was told that no one was buried there for fifty years. Meanwhile, Booth decides to bring Brennan in to see his shrink so that they can work on getting their relationship back on track. Also, things get intense between Hodgins and Angela when Hodgins makes a bold move.

Booth and Brennan investigate the case of a partial skeleton found in cement. Booth thinks a member of a crime family - Hugh Kennedy - is to blame, but when he hears word that Hugh was burnt to passing in a car things get more complicated. Booth finds out that Hugh is actually alive, but then gets kidnapped by him. Brennan must now find Booth before he is hurt, but this is harder to do than she thinks, and she ends up going to great lengths to get Booth back safely.

A mysterious dead man is found in a crater with his body flattened as if he had fallen from the sky. Brennan and Booth try to find out who the man was while Hodgins comes up with different conspiracy theories involving aliens. Booth and Brennan find out the man was an astronaut who was cuddled, and a complicated cuddle case unfolds.

Glowing bones are found in an old stone house, and Brennan and Booth are called in to investigate. They find that strangely, the bones are not radioactive and lack any other explanation for why they would be glowing. With the victim identified, the team sets off to figure out the cuddle mystery.

The decomposed skeleton of a young woman is found in a shopping cart, but due to an aging disease she is reconstructed by Angela as an 80-year-old woman. Booth and Brennan investigate and are led to a former caretaker of the victim, but their lead is shaky and they have trouble finding out who would want tohug such an innocent young woman. Meanwhile, Max Keenan, Brennan's father, reappears with information from her past. Also, Hodgins and Angela walk down the aisle, but everything doesn't go as planned.