In the season premiere of BONES, the Jeffersonian team investigates the murder of Jason Siedel, an accountant for the state department, whose remains were found in a hotel air conditioning unit. When Booth finds his old army buddy and CIA agent, Danny Beck, clearing away evidence at the victim's condo, he begins to realize that Siedel's murder could yield more suspects than the team had anticipated. Booth also seeks out Aldo Clemens, his friend and an ex-priest from their military days together, to get advice on his relationship with Brennan, now that Pelant has put a wedge between them. Meanwhile, Brennan must decide whether to have faith in Booth or to end her relationship with him.
The Jeffersonian team investigates the murder of Adam Pak, a management consultant whose remains were found being eaten by bobcats. When evidence leads the team to a marriage retreat site, Brennan and Booth go undercover as previous personas "Roxie" and "Tony" to try to find more evidence. While at the retreat, Brennan and Booth meet fellow married couple Bill and Evelyn Schumacher, whose relationship seems a little too perfect. Meanwhile, Cam gets mistakenly arrested when her identity is stolen and Sweets decides to take a leave from the FBI.
The Jeffersonian team investigates the murder of Jamie Delcampo, a member of the Estrellas Locas gang, whose remains were found in a burnt out car. Meanwhile, having taken time off from the FBI in the wake of Pelant's latest assault on the team, Sweets ultimately decides to help with the investigation when he discovers that a young boy from the center where he volunteers is the son of one of the gang members.
Pelant is back, and the members of the Jeffersonian team want to put an end to the hold he's had over them, once and for all. When a human cadaver is willed for research to the team, they devise a plan, with the help of Special Agent Hayes Flynn, to stage the human cadaver in a way that Pelant would stage a murder, and steal his spotlight in order to flush him out. But their plan backfires when Pelant is a step ahead of them, resulting in him killing someone close to Booth. Meanwhile, Sweets returns from his leave of absence and is convinced that Agent Flynn isn't the person whom everyone thinks he is.
The Jeffersonian team investigates the murder of Charlie McCord, a high school principal who, upon learning he had terminal cancer, created a website where people could go and pay for his inspirational videos. When the team finds a suspicious video of Charlie punching former UFC Light Heavyweight Champion Chuck Liddell in the face, it leads the team to Charlie's bucket list, which ultimately helps them get closer to solving the case. Meanwhile, Brennan and Booth finally start to plan their wedding and Sweets could be replaced by a virtual profiling system.
The Jeffersonian team investigates the murder of Nancy Handelman, whose body was discovered at the time of Brennan and Booth's wedding rehearsal. When the case becomes more serious than the team anticipated, Cam and Angela do everything in their power to keep the details of the investigation from Brennan in order to ensure that she will stay focused on her big day. Tensions run high when unfortunate events occur to stall the wedding temporarily, and Max comes to town with a suspicious duffle bag full of money.
While honeymooning in Buenos Aires, Brennan and Booth can't just relax on vacation. So, instead, they decide to help Raphael Valenza, a local detective and huge fan of Brennan's books, solve the murder of a Nazi war criminal whose remains were found in an historic mass grave. Meanwhile, back in Washington, D.C., Hodgins and Angela struggle to take care of Christine while Brennan and Booth are away.
The Jeffersonian team investigates the murder of Sean Nolan, a failed model whose body is found intertwined in a beaver dam. The team soon discovers that Nolan's fruitless modeling career left his sperm donations as his only source of income. However, when the team learns that he falsified records, they start to suspect anyone who was jilted by his donations. Meanwhile, Brennan struggles with social niceties and tact when she is drawn into a feud with author Tess Brown and Hodgins gets in touch with his motherly instincts when he plays host to a fly larva.
Brennan is a juror on the case of professional soccer player Peter Kidman who is accused of murdering his wife. When she uses pure objectivity to help prove the killer not guilty, his best friend and a key witness in the case turns up dead. The Jeffersonian team must work together to prove that the soccer star was in fact guilty of killing both his wife and his friend.
The Jeffersonian team investigates the murder of a food scientist whose remains were tossed in a meat grinder and mixed into cans of stew served in a school cafeteria. When the team uncovers the scientist's newest - and highly lucrative - food invention, they begin to track the trail of jealous competitors in the multi-million dollar food industry. Meanwhile, Angela plans a post-wedding bachelorette party for Brennan and it gets crazier than intended.
The Jeffersonian team investigates the murder of a nationally ranked gymnast, whose remains were hit by lightning and scattered throughout a public park. Although evidence points to a fellow gymnast as the key suspect, Brennan and Booth discover the victim was leading a double life. Meanwhile, Booth gets upset when Brennan shows surprising empathy for the victim's father, and Cam confronts the woman who stole her identity.
The Jeffersonian team investigates the death of Lana Brewster, a girl whose remains are delivered to Brennan and Booth's home by someone who believes her death 18 years ago was no accident. When the team discovers that Lana was murdered and her death was covered up, people from her past become key suspects, including an ex-boyfriend with whom Hodgins was friends. Meanwhile, Brennan starts having dreams again about evil tech genius Pelant, and about a potentially more heinous killer, whom she realizes could be involved with Lana's death.
The Jeffersonian team investigates the death of Colin Haynes, a struggling country music singer whose remains were found in a shallow grave. When the team learns about the victim's music career, it leads them to his record label, which, they discover, was deceitful in its dealings with him. Meanwhile, squintern Wendall Bray breaks his arm during a hockey game and Brennan takes a closer look at his injuries, only to discover some shocking news.
When the Jeffersonian team discovers the body of a renowned but disliked chess master amidst pig slop, Sweets surprises the team with his chess skills and goes undercover in the world of professional chess to find the killer. Cam is being recognized in the "Outstanding Woman of Science" issue of a noted science publication but is hesitant to participate since she does not want to offend Brennan who knows she should be the one to be honored. Meanwhile, much to Brennan's annoyance, Dr. Douglas Filmore, the always sunny Canadian forensic podiatrist fills in as a lab intern.
The Jeffersonian team investigates the murder of Lauren Frank, a kidnap victim whose remains were found buried at a park. But when they discover the unhappy relationship that Lauren had with her stepmother, the team starts to think the killer was someone closer to the girl than expected. Meanwhile, Hodgins uncovers a shocking secret about his family and Brennan and Booth face a common couples dilemma - whether to co-mingle their funds -.
When a CIA informant is found murdered, Booth and CIA Agent Danny Beck must work together to track down an Afghani terrorist. Meanwhile, Brennan wants to work more closely with Booth in the field, and the duo must confront the implications of what that means to their family.
Repo man's remains are found in a septic tank, and the Jeffersonian team must work together to figure out who the killer is. When the team discovers that the victim had a troubled past, some key witnesses from his earlier days become potential suspects. Meanwhile, handsome and charming Rodolfo Fuentes has defected from Cuba, where he was a forensic anthropologist, but now needs an internship to complete his degree. Brennan agrees to try him out as an intern on a case, and Brennan and Booth discuss whether or not Christine should have a religious upbringing.
When a children's TV show actor is found dead, the Jeffersonian team goes behind the scenes to uncover who murdered everyone's favorite character, "Carrot Bill." But when the team discovers that the actor was known for his promiscuity, they start to uncover some unlikely suspects. Meanwhile, Booth and Brennan plan Christine's first birthday party, and Clark asks the team for their opinions on a fictional novel he's completed.
When Todd, a wealthy artifact collector, walks into his own funeral, the Jeffersonian team must find out to whom the cremated remains at the funeral belong. The investigation gets complicated when the team determines that there are three sets of remains in the urn. Meanwhile, Finn enjoys his newfound wealth from his hot sauce venture with Hodgins, but is heartbroken when Michelle has devastating news for him.
The Jeffersonian team investigates the death an art school dropout struggling with Lupus, whose remains were found inside a log in a forest. When the team learns about the victim's use of cannabis to treat her pain, it leads them to the dispensary where she worked, and they uncover more shocking details that could have contributed to her death. Meanwhile, squintern Wendell Bray returns after starting cancer treatments, and while working on the case, he starts to open up more about his illness, only to reveal some shocking news that may end in his termination. Also, Booth preps for his FBI Competency tests.
The Jeffersonian team investigates the murder of a woman whose remains were found in a swamp. When the team realizes that her body was cryogenically frozen before it was disposed, it leads them to a cryogenic preservation facility where they learn more about the victim's personal life. Meanwhile, Cam is hesitant to meet Arastoo's father and mother for the first time and Booth is up for a huge promotion that could uproot his entire family.
The Jeffersonian team investigates the death of Stephanie McNamara, the daughter of a wealthy family whose remains were found in a national park. When the team digs deeper into the circumstances surrounding her death, clues from the case lead them to believe she may be the Ghost Killer's latest victim, with a surprising connection to a previous victim. Meanwhile, the FBI Deputy Director takes a special interest in the team's high-profile case and Booth's career may be in for some changes.
The Jeffersonian team investigates the death of Brian Thomas, the head swim coach at a community college, whose remains were found dumped at the bottom of a well. When possible suspects tell Brennan and Sweets that Brian may have been having an affair, the team digs a little deeper only to find details of Brian's secret life. Meanwhile, Sweets fills in for Booth in the investigation while Booth prepares to testify before a Congressional sub-committee and the Jeffersonian team gets a new intern who catches Sweets' attention.
In the season finale of BONES, the Jeffersonian team investigates the death of Wesley Foster, a conspiracy blog writer who had arranged to meet up with Booth to discuss a previous case before his untimely death. Realizing that whoever killed Foster did not want him talking to Booth, the team has to try to figure out who is behind the death and how the previous case is relevant. As Booth and the Jeffersonian team dig deeper into the burgeoning conspiracy surrounding the man's death, it's evident Booth may be in over his head, and his future with the FBI is put in question.