A good-hearted, unusually gifted orphan named Reynie Muldoon enters a competition to win a scholarship to the prestigious Boatwright Academy. While undergoing a grueling series of tests, Reynie joins forces with two other uniquely gifted orphans, Sticky Washington and Kate Wetherall, and the three of them work together to tackle the challenges in their path. The children are introduced to a fourth gifted orphan, Constance Contraire, and finally to the enigmatic Mr. Benedict.

Mr. Benedict lays out the world-changing stakes of his top-secret mission to Reynie, Sticky, Kate, and Constance: The Emergency is out of control, and the only way to stop it is to infiltrate the mysterious L.I.V.E. Institute on Harbor Island. Our young heroes embark on an undercover operation as transfer students at the school, and learn to navigate unfriendly fellow students, bizarre, nonsensical classes, and a shockingly familiar Headmaster.

The kids of the Mysterious Benedict Society come to a grim realization about Dr. Curtain’s methods of keeping secrets. They also learn the dire consequences to the mission if they were to slip to the bottom of their classes: they would be kicked out. After receiving a message from the children, Mr. Benedict and his crew investigate his possible connection to Dr. Curtain. The children resolve to learn more about the elite Messenger program at the school.