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.
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.
The team devises a plan to use a donated cadaver to draw out Pelant; Sweets returns to work and believes Agent Flynn isn't who he seems.
The team investigates the murder of a high school principal who was dying of cancer; Brennan and Booth plan their wedding; a virtual profiling system threatens Sweets' job.
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.
Unable to relax on their honeymoon, Booth and Brennan decide to help a local detective solve the murder of a Nazi war criminal; Hodgins and Angela look after Christine.
The team suspects that a man who made his money donating sperm was killed by a recipient who learned his records were inaccurate; Brennan enters a feud with a fellow author (Nora Dunn).
A key witness turns up dead in a case for which Brennan is a juror, so the team works to discover what has happened.
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 also track the trail of jealous competitors in the multi-million dollar food industry. Meanwhile, Angela plans a post-wedding bachelorette party for Brennan, which 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 team investigates when the remains of a girl who died 18 years earlier are delivered to Brennan and Booth's house; Brennan dreams about Pelant.
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 team discovers a renowned chess master in pig slop, Sweets goes under cover in the chess world; a science magazine honors Cam; Dr. Douglas Filmore fills in as 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 (guest star Freddie Prinze Jr.) 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.
When the remains of a repo man are found in a septic tank, the team learns he had a troubled past; a forensic anthropologist (Ignacio Serricchio) who has defected from Cuba needs an internship.
When an actor known for playing a popular character on a kids' TV show is murdered, unexpected suspects are discovered; Brennan and Booth plan a party for Christine's birthday; Clark asks for opinions on his novel.
When a wealthy artifact collector walks into his own funeral, the team must determine the real identity of the deceased; Finn's new hot sauce venture is making big money.
The remains of a former art student are found in a log in a forest; Wendell returns after beginning cancer treatments; Booth prepares for an FBI competency test.
The team investigates the death of a woman whose body was cryogenically frozen before being dumped in a swamp; Cam is nervous to meet Arastoo's parents; Booth is up for a promotion.
When the remains of a woman from a wealthy family are found in a national park, the team thinks she may be a victim of the Ghost Killer; Booth's career might be in for some changes.
When the head swim coach of a community college is found dead at the bottom of the well, possible suspects think he may have been having an affair; Sweets covers for Booth in the investigation as Booth prepares for a congressional subcommittee.
The team investigates the death of a man who had offered Booth information on a possible government cover-up related to a previous case, but was killed before their meeting took place. 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.