Episode 39 of "Bones"
s02e17 The Priest in the Churchyard

A water main bursts in the middle of the night at the historic St. Agathas church cemetery, leaving the cemetery grounds littered with coffins and their once-peaceful inhabitants, and Brennan is called in to identify and help re-inter the remains. Father Matt, a newly installed priest, has informed Brennan and Zack that the last burial in the cemetery took place over 50 years ago, but Brennan finds a skull buried less than five years ago, leading them to believe the body was buried to hide a murder. After meeting some opposition from cantankerous head priest Father Donlan, Brennan and Zack deem the once-consecrated ground a crime scene. They take the remains back to the Jeffersonian, where Booth is offended by Brennans lack of respect for his or anyone elses religious beliefs, and the two struggle to find their rhythm, which has been disrupted ever since Sully left. Booth insists Brennan come with him to see his therapist, Dr. Wyatt, in hopes that Wyatt can help their relationship and get things back on track between them. Meanwhile, Hodgins and Angelas romance heats up and Hodgins makes a bold move to advance things between them, taking Angela completely off-guard. When Booth and Angela return to the church to pass out sketches of the unidentified murder victim from the cemetery, a young parishioner identifies the sketch as the former parish priest Father Matt had replaced a short time ago. As Father Matt grows mysteriously ill and Brennan and Booth attempt to trace the details of the murdered priests disappearance, they must determine who is playing God and taking lives into his own hands.