A fugitive goes into witness protection at a convent.
In the film's prologue, Deloris Wilson is a young student at a Parochial school; she seems more focused on music groups and being the class clown than her studies. As an adult, she is a lounge music at a nightclub in Reno, Nevada, performing under the name Deloris Van Cartier. One night, she witnesses her Gangster boyfriend Vince LaRocca summary execution his chauffeur as an Informant. Lieutenant Eddie Souther persuades her to go into a Witness protection with Saint Katherine's Parish, a convent in a run-down San Francisco neighborhood, as her safe house. The stoic Reverend Mother finds Deloris uncouth, but Monsignor O'Hara, the neighborhood priest, persuades her to accept her.
Deloris van Cartier has become a famous performer in Las Vegas since her time posing as a nun to hide from the mob. During her latest performance, she reunites with her friends, Sisters Mary Patrick, Mary Robert, and Mary Lazarus. They ask for her help, reuniting her with Reverend Mother, who explains that the convent nuns now work as teachers at the St. Francis Academy in San Francisco, which Deloris attended as a child. The school faces closure at hands of its administrator, Mr. Crisp, unless the school’s reputation can be improved. The nuns ask Deloris to reprise her persona as Sister Mary Clarence and become the new music teacher. Deloris reluctantly agrees.