Olive takes Pigby truffle hunting and unearths a large specimen. The convent's truffle expert and Olive's friend, Sister LaRue, approaches and takes the truffle away. She makes it into a candy then her and Olive talk about how truffles are so wonderful because their chemistry resembles sex.
Ned goes to Chuck's apartment and when she opens the door, a man named Cyrus Pennybaker walks out. Chuck shows Ned her unfinished family tree drawing that she started in grade school, but never got to finish since her parents had died and her aunts didn't know anything about her family. Chuck explains that she hired Pennybaker to help her find her ancestors.
Back at the convent, Olive prays to God saying she plans to stay there for the rest of her life unless he gives her a sign otherwise. Suddenly Sister LaRue drops out of the sky, to her death. Mother Superior gathers the nuns and says Sister LaRue committed suicide. Olive interjects that she just saw her and she seemed so happy.
Olive decides to go to Emerson with her case. She tells him that she has no money, but can pay him with prayers. Feeling like he needed all the prayers he could get to find his daughter, Emerson agrees to help. Olive makes it clear that he can't let it be known that he knows her and Ned and Chuck can't help.
Emerson meets up with Olive at the convent's bell tower with Ned and Chuck. Ned and Emerson are dressed as priests and Chuck as a nun. Mother Superior and Father Ed arrive and Emerson says they are from Italy to look into the death of Sister LaRue. They ask Mother Superior if there was any reason she would kill herself. She tells them that the truffle harvest was low causing the convent to run out of money. Emerson asks to see the body. Olive asks to go with, but Mother Superior says no and hands her a list of penances to complete.
Ned isn't sure if he can wake Sister LaRue up in front of the Jesus and Mary statues, but Emerson convinces him. LaRue wakes up and realizes that the afterlife was all a crock. Using extremely foul language, she says someone stole her diamond and pushed her out of the tower. She tries to run away, but Ned grabs her and returns her to being dead.
Ned finds out the Sister LaRue was Dr. Linda Frank, a mushroom scientist, before she joined the convent. Chuck tells Ned that while he was looking into LaRue's records, she was looking at Olive's. Chuck is convinced that Olive ran away because of her and she wanted to know why, but the part asking why she wants to join the convent was left blank. Ned and Chuck then notice a secret door in the room they're in. They hear someone coming, so they hide. Mother Superior walks through the door.
In LaRue's room, Emerson tells Olive that LaRue was murdered, which makes Olive upset. Emerson then notices a secret door in the wall. They open it and a stockpile of convent contraband falls out. Another Sister walks in and admits that she used to get stuff from LaRue in exchange for doing LaRue's chores. Ned and Chuck show up and Olive runs out.
They figure that LaRue had smuggled diamonds in for herself and Mother Superior found out about them. Since the convent was low on money, Mother Superior might have killed LaRue to take her diamond for convent cash.
Mother Superior asks Chuck what made her take up the veil. Chuck, after some confusion, starts to tell Mother Superior about losing her parent. She asks to use her phone and calls Mr. Pennybaker.
Emerson and Ned go to the truffle cellar to try to find more answers. They notice a brick wall that has a recently added patch. Emerson breaks through the bricks and they discover a tunnel that leads to a door. They figure that was LaRue's way to smuggle things in and out of the convent, so they follow to see where it goes.
Emerson and Ned end up in a gourmet kitchen. They look through a window and see a butcher covered in blood. The butcher ties them up and threatens to kill them. Ned consoles him and the Butcher starts to tal