Brennan and Zack go to a church graveyard to identify bodies that were exposed due to a water main breaking. Father Matthew Sands (the intern priest) mentions experiencing stomach aches over the past few days. Father William Donlan (the original priest) shows up, clearly upset that Father Sands didn't inform him that he was planning to give Brennan the burial records. Brennan informs Father Donlan that they found a skull buried no more than 5 years ago. Father Donlan says that no one has been buried there for years. Brennan decides to inform Booth, and announces that the graveyard is a crime scene.
Back at the lab, Booth and Brennan argue about Brennan not being polite with the priest. The argument takes a religious turn, and Booth tells Brennan that it isn't about religion, but that they have working issues that are affecting their relationship. They agree to get back on the murder case.
Cam and Hodgins find out that the reason that the water main broke was because someone was digging in the cemetery and hit it. Angela shows up with the face of the victim. Cam orders them to send their findings to Booth while she goes and investigates the blood.
In the church garden, Brennan argues with Father Donlan about the date of the burial of the victim. Lorraine Bergin (the perish administrator) invites Booth and Brennan to go inside and speak to Father Sands. Booth shows him the sketch of the victim but he doesn't recognize it.
Inside, Father Sands says that he started some new activities since he arrived. Lorraine mentions that in a month she will complete 23 years at the parish. Father Sands offers bringing the sketch to the next mass to ask the attendees. Booth argues with Brennan about insulting the priest. He asks Brennan to go see Dr. Gordon Wyatt with him. She first refuses then says yes.
Hodgins and Angela are flirting, and Hodgins asks her to move in with him. She refuses. Cam walks in; she informs them that they have been exposed to a fungus that causes nausea, fever, and maybe death.
In therapy, Booth and Brennan are bickering in front of Dr. Wyatt. Dr. Wyatt says that they aren't fighting about religion but they are arguing about an issue that he will find out about and help them deal with.
Angela goes with Booth to church; she keeps interrupting him while he prays. The attendees are shown the sketch. James Levay, a teenager, recognizes him as the ex-intern priest, Father McCourt. According to Lorraine, the victim left a note saying that he was leaving the parish. The squints conclude that it didn't have to be a shovel that killed Father McCourt but any heavy valuable object.
In the lab Dr. Wyatt tells Booth that his problem with Brennan is not knowing what will catch fire in the lab and where to stand. Enzo (a church attendee) tells Booth and Brennan that they should talk to James (the boy who recognized Father McCourt), because everybody suspected Father McCourt of being a pedophile. James denies that and says that Father McCourt never treated him wrong, but was a very close father figure and a best friend. He tells them that Father Donlan was pretty cruel with Father McCourt. Father Donlan admits it and says that he's strict with all the priests.
The lab finds out that something silver was used to hit and kill the victim. Brennan talks to Dr. Wyatt in the interrogation room. They agree that she wants to be more like Booth. At the church, Brennan takes the chalice, claiming that it's the object used to murder the victim. The lab confirms it; they also conclude that Father McCourt was poisoned. Booth and Brennan talk to Father Sands; he tells them that he didn't know Father McCourt even though they went to the same seminary.
Booth and Brennan are arguing over lunch. Dr Wyatt joins them. He tells them that they think Brennan's reason to not go with Sully was her attachment to Booth. He denies it and tells them that she didn't go because she can't lead a purposeless life at this stage of her existence. He leaves and they conclude that Father Sands was poisoned just like Father McCourt. The lab confirms their conclusion.
Brennan tells Angela what Dr. Wyatt said. Angela suggests talking to him about her problem with Hodgins' asking her to move in with him.
Father Donlan falsely confesses that he killed Father McCourt, and Booth doesn't believe him. The priest agrees to back down on one condition: if he gets the confession from the murderer. Lorraine confesses to the murder to Father Donlan.
Angela and Brennan go to talk to Dr. Wyatt. He explains to Angela why she shouldn't move in with Hodgins. Booth arrives to pick up Brennan, leaving Angela alone with Dr. Wyatt. Angela tells Dr. Wyatt that she knows the real reason Brennan didn't go with Sully was because of Booth. He denies it but she convinces him not to pretend that she's wrong.