Seeley Booth returns to active duty with the FBI after being certified by Dr. Sweets and wonders if his feelings for Brennan are real or if they are just the effects from his brain surgery. Angela’s psychic Avalon (Cyndi Lauper) leads Booth and Brennan to a crime regarding bodies being buried under a fountain in Washington, one of which is Avalon’s younger sister. Wendell’s scholarship funds are cut due to budget constraints at the Jeffersonian but ‘annoymous’ donations (which is obvious to him was done by Drs. Saroyan, Hodgins, Brennan and Angels) let him stay. The team investigates the remains of a teenage Amish boy who disappeared two months prior to Rumspringa, where he would explore the outside world. They later discover the boy was a piano prodigy and kept it as a secret from his family. Cam deals with parenting issues as she believes her stepdaughter Michelle might be having sex, leading Booth to help out. The team investigates the remains that were found in a barbecue pit during a suburban neighborhood block party, leading to several secrets about the residents in the neighborhood being exposed. Iranian intern Arastoo confesses to everyone that he has been faking his accent and explains why he did so. Booth’s son Parker seems concerned that his dad does not have a girlfriend.
A mysteriously charred body that is found on an electrical fence turns out to be a mummified Egyptian royal that was loaned to the Jeffersonian from the Egyptian government & the curator that was prepping the mummy is found murdered. Booth’s supervisor, the assistant director of the FBI, Andrew Hacker, shows interest in Brennan and they later go on a date. Sweets convinces Brennan to give Daisy another chance, having her return to the Jeffersonian as an intern.Wendell & Angela begin a brief relationship. ooth, still dealing with effects from his brain tumor, has problems with his aim and must be re-certified for FBI marksmanship. He then seeks advice from Dr. Gordon Wyatt (Stephen Fry), who is now a chef, in hopes of overcoming the problem. Booth and Brennan travel to Roswell, New Mexico, after possible alien remains are found. Hodgins deals with his jealousy after Angela and Wendell confess they are in a relationship.
The Jeffersonian lab is put on lock down by government agents led by Mr. White when they demand Brennan and her team identify of cause of death for a highly classified set of remains. Cam finds a positive pregnancy test in the woman’s bathroom and after all the women deny it is theirs, she believes it might be Michelle’s, her stepdaughter. After, Angela confesses to Cam that it was actually hers, but did not want anyone else to know. In the interim, Cam had it tested again, and reveals to Angela that it was a false positive, meaning she is not pregnant. The team eventually come to believe the set of remains they are working on are actually that of assassinated President John F. Kennedy. The case causes tension between Hodgins and Booth as the information they gather supports the conspiracy theory about a cover-up, whereas Booth is a patriot and believes in the government. Mr. White terminates the testing before completing the cause of death, leaving the results inconclusive. To help Booth, Brennan performs a test on one of bones, proving it is not JFK; although Cam tells her she knows what she did was for Booth, and there is still a possibility it was JFK. A TV news report says the request to exhume the bones of JFK has been denied.
Booth’s brother Jared & Booth clash over the past of the former’s new girlfriend. While Dr. Sweets is on a subway train, a stranger tells him he has just been cured of leukemia, then the train is thrown off its tracks as a water main breaks, causing havoc inside the train leading to death of the man who had just been cured of cancer. Sweets deals with the near-death experience feeling it was a message to live his life fully, leading him to propose to his girlfriend Daisy. We also learn of how Booth & Brennan first met on a case and also Booth tells Brennan that he loves her. At a case during her high school reunion Brennan learns how lucky she is to have the friendships she has today. Hodgins and Angela wind up in jail after some reckless driving and have to work the case from the jail cell. After spending quality time together, they realize they are still in love. Hodgins subsequently proposes to Angela and they are married by the judge who hears their case.
Brennan, Booth, and Hodgins are forced to drop their own charges against Taffet once they discover the missing remains of a young boy who was killed by the Gravedigger, so they could work and testify against Taffet. This evidence proves successful and the jury convicts Taffet of kidnapping and murder, but Taffet warns Brennan “that it’s not over”. In the season finale, many of the characters begin to embark on trips that will take them out of the country for one year, intending to return and pick things up where they left off one year from that day. Temperance, along with Daisy Wick, go to the Maluku Islands to study a full set of interspecies hominid remains that could be a crucial link in the evolutionary chain. Booth returns to the Army as a Sergeant Major to train soldiers in apprehending insurgents. Meanwhile, newlywed Angela and Hodgins decide to travel.