Mary Clarence attempts her first lessons in the music class, finding the students unruly and rude. Among the students is the ringleader Rita Watson; preachy Ahmal; rap artist Frankie; Sketch, who sleeps a lot due to heavy work; and fashionable Maria. Upon learning the school will close at the conclusion of the current term, Mary Clarence rallies the nuns and monks to find a way to improve the school to keep it open. Like Reverend Mother before him, Father Maurice finds himself in conflict with Mary Clarence and her unconventional ways, but Reverend Mother reassures Father Maurice that Mary Clarence's presence will help.
Mary Clarence properly takes control of her class, prompting Rita to walk out. When the class breaks out in spontaneous singing, showing their true potential, Mary Clarence decides to turn the class into a choir. At first, the class is skeptical, but change their minds when finding out the school will close.
When Mary Robert finds Rita singing before a friend, she and Mary Clarence convince her to return to classes. The class rebuilds the music room and becomes a successful choir under Mary Clarence's guidance, with Rita returning to become a lead singer alongside Ahmal. The choir performs before the school and receives a standing ovation. After the nuns find trophies revealing the school had won the state choir championship before, they and Mary Clarence enter the choir in the competition, with Father Maurice's reluctant permission. However, Rita's strict mother Florence refuses to let her daughter attend, believing a career in music to be a dead end. Rita rebels, forging her mother's signature on the parental consent form to follow her dreams, leaving her mother an apologetic letter. Shortly after the choir leaves, Mr. Crisp discovers Mary Clarence is no nun and convinces Father Maurice to withdraw them from the competition. They race after the choir with the monks, hampered by Father Thomas's reckless driving.
At the championship, the choir is intimidated by the competition and considers quitting, but they change their mind after Mary Clarence sternly lectures them, reminding them how far they have already come. Father Maurice appears to inform the choir of his decision, but, surprised by the choir's robes, changes his mind and allows them to go onstage. The other monks lock Mr. Crisp in a closet to prevent him from revealing Mary Clarence's true identity to the representatives of the diocese who had come to the competition. Rita arrives onstage, briefly getting stage fright when she spots her mother in the audience, but leads the choir into a modern, hip-hop-inspired rendition of Joyful, Joyful We Adore Thee. The choir ultimately wins the championship, and the diocese representatives, impressed by the choir's performance, allow the school to remain open. They even give the shocked Mr. Crisp a promotion (against his wishes) when Reverend Mother makes it look like he came up with the idea to attend the competition.