Father O'Malley, a kindly and optimistic priest, is assigned to St. Mary's, a run-down parochial school on the verge of being condemned. Upon arrival, he clashes with the headstrong Sister Benedict, who has a very different approach to education and discipline. Despite their differing philosophies, both are deeply committed to saving the school and providing the best for the children in their care. They face numerous challenges, including dealing with a grouchy businessman, Horace P. Bogardus, whose plans threaten the existence of the school.

Over time, Father O'Malley and Sister Benedict begin to understand and respect each other's methods, working together to build a better future for St. Mary's. Their shared dedication inspires the students and the community to come together in support of the school. As they navigate through these difficulties, they impart valuable lessons about faith, teamwork, and perseverance. Their journey is filled with moments of warmth, humor, and heart, ultimately transforming the school and its surroundings in ways they never expected.