The Trouble With Angels opens on the first day of school for a new batch of students at St. Francis Academy, run by a very strong-willed Mother Superior (Rosalind Russell). She is used to having things her way, but she may have met her match in the headstrong and independent Mary Clancy (Hayley Mills) and her newfound friend, Rachel Devery (June Harding). Mary, easily bored and ready to rebel at the drop of a hat, comes up with an endless series of "scathingly brilliant" schemes designed either to amuse her and Rachel, torture insufferable schoolmate Marvel-Ann, or in some way help them get ahead. Rachel, who would never come up with such ideas on her own, is delighted to go along with them. The duo starts right away by convincing several of the girls to join them in giving fake names to the sisters that register them. Future escapades include guided tours of the nuns' living quarters, illicit cigarette smoking that brings about the fire brigade, replacing sugar with soap bubbles, and many others. Several times the Mother Superior is on the brink of expelling the girls, but she relents, knowing something of their home lives and that they will benefit from the more nurturing environment of the school. By the end of the film, the girls have indeed grown, and Mary, in particular, has developed a special love for the Academy.