2x01 - The Titans On The Track
The Team Investigate a Bullet-Train derailment causing the death of a senior senotor and Brennans only link to finding her father is killed in prison.

2x02 - The Mother and Child In The Bay
A Dead woman and her fetus are found in Delaware bay, The Woman had mysteriously disappeared a year ago. The Murder suspect is the woman's husband but he soon disappears before Booth and Brennan have a chance to catch up with him causing Booth to call for a manhunt

2x03 - The Boy In The Shroud
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.

2x04 - The Blonde in the Game
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 death points to a convicted serial killer on death 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 killer'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.

2x05 - The Truth In The Lye
There are two suspects with the same motive when Booth and Brennan investigate the murder of a man found in a bathtub full of chemicals. They soon discover that he had two wives and a girlfriend.

2x06 - The Girl In The Suite 2103
Booth and Brennan investigate a death due to an explosion in a hotel. Things get complicated when the main suspect of the investigation appears to be protected by diplomatic immunity.

2x07 - The Girl With The Curl
The team investigates the death 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 killer. Back at the lab, Hodgins and Angela go on a date that actually goes well, despite what everyone else predicted.

2x08 - The Woman In The Sand
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 was killed 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

2x09 - Aliens In a Spaceship
The bodies of twin teenage boys, kidnapped five years earlier, are discovered. Booth and Brennan follow the trail of a notorious serial killer, known as the Grave Digger. His M.O. is to kidnap, bury his victims and 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. Both are forced to solve their own kidnapping from an underground grave.

2x10 - The Headless Witch In The Woods
While investigating the death 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.

2x11 - Judas On A Pole
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 30yr old case and links back to Brennans father

Brennan's brother, Russ, informs her of a phone call he received from their father, warning him that they are both in danger. Soon after a priest contacts Brennan telling her that her father insists on she and Booth to drop their case.

They determine that the body found was actually an ex-FBI agent, who was tracking Russ to kill him. Hence giving reason to Brennan's father's warnings. The deeper they get into their case the more they learn and finally make a shocking discovery that can cause serious repercussions for Booth and his career.

Zack must defend his dissertation to obtain his doctorate, asking help from a colleague.

2x12 - The Man In The Cell
Booth and Brennan are ordered to the cell of serial killer 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.

2x13 - The Girl In The Gator
Brennan has to work with another agent, Agent Sullivan, while Booth needs to see a therapist. They investigate the death 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.

2x14 - The Man In The Mansion
Booth and Brennan investigate the death 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 to the case itself. Due to this, Brennan must make an important decision about her team. Booth, although cleared by Dr. Wyatt (guest star Stephen Fry) to use his gun, must continue to meet with the psychiatrist.

2x15 - Bodies In The Book
Brennan and Booth have to solve three cases that are all highly similar to those in Brennan's new book on the bestseller list.

2x16 - The Boneless Bride In The River
The team investigates the death of an Asian woman without any bones left in her body. Sully proposes something to Brennan that she does not expect.

2x17 - The Priest In The Churchyard
A water main bursts in the middle of a cemetery, leaving lots of coffins to litter the grounds. Brennan is called in to identify the remains so they can be reburied. When she finds the remains that have only been there for five years after being told no one was buried their in fifty years. Booth decides to bring Brennan to see his shrink so that they can work on getting their relationship back on track. Things get intense between Hodgins and Angela, when Hodgins makes a bold move.

2x18 - The Killer In The Concrete
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 death 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

2x19 - Spaceman In a Crater
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 murdered, and a complicated murder case unfolds.

2x20 - The Glowing Bones in the Old Stone House
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 murder mystery.

2x21 - Stargazor In a Puddle
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 to kill 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.