Air date: 9/17/09

Booth returns to the FBI after being certified by Dr. Sweets and wonders if his feelings for Brennan are real or if they are just the effects form his brain surgery. Angela's psychic Avalon leads Booth and Brennan to a crime regarding bodies being buried under a fountain in Washington, one of which is Avalon's younger sister.

The Bond in the Boot

Air date: 9/24/09

Booth and Brennan investigate a highly classified case regarding the death of a man and a CIA analyst which revolves around the unknown contents of a briefcase. Funding is cut back at the Jeffersonian, leaving Wendell's scholarship at risk, but anonymous donations are made, saving his internship. Booth deals with effects of his coma, causing him to relearn how to fix the broken pipes for his sink, instead of paying for a plumber.

The Plain in the Prodigy

Air date: 10/1/09

The team investigate 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 Beautiful Day in the Neighborhood

Air date: 10/8/09

The team investigate 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.