Deloris Wilson (Whoopi Goldberg), a black woman who has chosen the stage name Deloris Van Cartier, is a Reno, Nevada lounge singer, she, the lead in a girl trio, in which she also chooses and arranges the music and choreographs the shows. She is a wisecracking, showy woman who has always loved music. She, however, only has her current job being hired by her married lover, Vince LaRocca (Harvey Keitel), to sing in his casino's lounge. She learns of Vince's true business as a gangster when she walks in on him killing one of his employees who wronged him. As a witness to the murder, Deloris goes on the run to the police, Lieutenant Eddie Souther (Bill Nunn), who has long been running an operation to get enough evidence to put Vince behind bars, this murder, which could be the metaphorical nail in Vince's coffin. However, Vince has put a contract out on Deloris' life to prevent her from testifying against him. As such, Eddie has to hide her until the trial, which will be at least two months. Where Eddie chooses is St. Katherine's, a poor Catholic parish and convent in a tough neighborhood in San Francisco. The convent's Mother Superior (Dame Maggie Smith) reluctantly takes Deloris in, that reluctance as Deloris is not anywhere near being close to looking or acting like a typical nun. Furthermore, the Mother Superior does not tell any of the sisters Deloris' true identity or the real reason for her being at St. Katherine's. With the Mother Superior cloistering the sisters behind the convent walls to pray for the salvation mostly of down and out of the neighborhood while keeping the sisters safe from harms of the outside world, there is an immediate and continual clash of wills between her and Deloris. Deloris, as renamed Sister Mary Clarence, does have an effect on two of the sisters, Mary Patrick (Kathy Najimy), a perpetually perky woman, and Mary Robert (Wendy Makkena), who always feels left behind in whatever is happening in life. The clash between Deloris and the Mother Superior leads to the Mother Superior restricting Deloris to one task at the convent, one that leads to good and bad changes at St. Katherine's, the bad most specifically in potentially leading Vince and his associates to Deloris. Those changes also bring the battle of wills between Deloris and Mother Superior to a head, unless each can see the positive in what is happening in relation to their life at the convent.
