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.