Season two starts off with Dr. Daniel Goodman leaving the team in the able hands of Dr. Camille Saroyan (Tamara Taylor), a first-rate pathologist who has been hired as the head of forensics at the Jeffersonian, and more importantly, Brennan’s boss. Dr. Goodman is on a long sabbatical as way of explaining Johnathan Adams’s departure from the show and is never seen again till date. What’s even more complicated is that Booth & Camille used to be lovers. Brennan and Booth investigate the site of a train wreck where the bodies of a senator and a high-profile businessman are found within the wreckage and it turns out that the businessman is actually alive and in a hospital and someone else’s body was used in the car. As the clues begin to unravel, the investigation gets more complicated when details of the man’s private life are revealed, leading Brennan and Booth to a private detective who may hold key information.
Next they investigate the remains of a woman and fetus washed up on the beach of the Delaware Bay; Carlie Richardson, a pregnant newly-wed whose mysterious disappearance one year ago had been a major national news story. However, the immediate prime suspect, Richardson’s husband, has also disappeared. Meanwhile, things get tense when Brennan and Cam struggle for power in their disagreement on work styles. Cam threatens to fire Brennan even if it costs her the whole Jeffersonian team. Then it’s the case of two young lovers, the product of the foster home system. Howard Epps is back in the fold again when skeletal remains of a young girl are found, and when brought back to the lab, the team recognizes this as the work of Epps. Brennan and her team scramble to decipher Epps’ cryptic clues as they try in a desperate effort to find his accomplice who has been killing for Epps and possibly save a next victim. The remains of a man dissolving in a bathtub of corrosive chemicals are found in a construction site, leading to finding out that the man had a double life with 2 wives & 2 families and a girlfriend!
Their next case brings them to judge Dolores Ramos, the Colombian judicial representative, who agrees to waive diplomatic immunity for the murder of young hostess. When the remains of a young beauty queen is found, the investigation leads Brennan & Booth to a fellow contestant who accidentally killed her meaner opponent and stuffed her body in a sewer pipe. Booth and Bones go undercover to infiltrate an underground fight circuit in Las Vegas. The team then investigate the murder of two kidnapped teenage twin boys who were placed in a spaceship-like capsule and buried alive underground. This is the beginning of the Grave Digger arc. Brennan and Hodgins find themselves victims of the “Grave Digger”, and Booth frantically searches for them as they slowly run out of oxygen underground. Next up is a myth about a witch in the woods. 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 hotel that housed Federal witnesses. This leads to Brennan finding out her father (played by Ryan O’Neal) and reunion with her brother Russ. Then Epps escapes and is after Brennan & Booth but is killed in a tussle over a balcony and Booth is unable to hold on to Epps, who falls to his death.
Booth is order to undergo an evaluation under a psychiatrist (Stephen Fry) when he angrily shoots at an ice cream truck clown. Brennan is paired up with Agent Tim Sullivan to investigate the apparent murder of a college student in the Everglades, which leads to a romantic interest among the two. Hodgin’s is pulled up for review when he holds back his involvement with the widow of a prominent Jeffersonian benefactor and helps in the investigation of the man’s murder. Three separate bodies are found murdered exactly the way Brennan wrote them in her new book. However, the killer’s method was different every time, leading the team to believe that it was not one but three killers. And then During Brennan’s vacation, a woman’s body is found with its bones removed. Meanwhile Sully tells Brennan he bought a boat and will be leaving for a year, at the end of the case, to tour the Caribbean; He asks Brennan to take a year-long sabbatical and go with him. At the end of the episode Sully sails off in his new boat, “Temperance”, while Brennan waves good-bye, as she has decided not to go.
Brennan & Booth then find out a murdered priest’s remains in a church graveyard and investigate the priests and administrator of the church and argue about the validity of religion. The team investigates the death of an astronaut who appears to have fallen to Earth from a high altitude. While Brennan and Booth question his associates at the Space Agency, Hodgins theorizes about a conspiracy involving extraterrestrials. Hodgins asks Angela to marry him but she refuses, asking him to keep trying. The next case is of a body whose bones are glowing but is negative for radioactivity. As the season ends Hodgins and Angela prepare for their wedding. Zack is asked to serve his country in Iraq. Brennan’s father, Max, tries to let her in on her past and brings her a 1993 video of her mother. Booth and Max get into a fist fight before Max surrenders to his arrest. However the couple cannot marry as a court reporter doing a routine background check finds out that Angela is still married to a man from a previous relationship, which she assumed hadn’t been serious. The couple escape embarrassment, leaving Brennan and Booth facing each other awkwardly at the altar. Hodgins and Angela prepare for their wedding. Zack is asked to serve his country in Iraq. Brennan’s father, Max, tries to let her in on her past and brings her a 1993 video of her mother. Booth and Max get into a fist fight before Max surrenders to his arrest.