The Mysterious Benedict Society is reunited when Mr. Benedict invites the children to his mansion with the expectation of sending them on a globe-trotting scavenger hunt. But when Mr. Benedict and Number Two go missing while in Europe, the kids defy the adults' orders and sneak off to find them on their own. Mr. Benedict and Number Two have been kidnapped by Dr. Curtain, who has bounced back after the failure of The Emergency by claiming credit for its destruction and capitalizing on that fame to push his new Happiness Revolution – which is really a subtle form of manipulation creating an artificial feeling of euphoria. Dr. Curtain and his Happiness acolytes live on a compound in rural Italy and are making plans to spread their joy to the world. The kids cross to Europe by stowing away on a ship and use the clues left for them by Mr. Benedict to get closer to finding out the truth of their whereabouts. Meanwhile, the children are pursued by both the adults of the Society (Rhonda, Milligan, and Ms. Perumal) who are concerned for their safety, as well as a Water Polo Team with nefarious intentions. The intrepid members of The Mysterious Benedict Society scour Western Europe as they piece together the mystery in front of them, dodging unexpected dangers and new and old adversaries at every turn. When everyone reunites at Dr. Curtain's compound, they realize that Curtain's methods lead to unexpected side effects. The Society enacts a swift escape and retreats to a safe location to prepare for a final confrontation, but they must find a way to undo the damage of Curtain's methods on some of their own before it's too late.

When the kind-hearted orphan Reynie Muldoon wins a scholarship to the prestigious Boatwright Academy, his life is changed forever… just not in the way he imagines. Alongside a group of gifted (be them odd) youngsters, Reynie undergoes a series of grueling tests to prove his mettle. After overcoming their initial trials, Reynie and his new companions, the quiz-show champion Sticky Washington, the circus performer Kate Wetherall, and wild-card Constance Contraire are tasked with a mission far more perilous than they could have imagined. Their benefactor, the mysterious Mr. Benedict, tasks them with infiltrating the L.I.V.E. Institute. Their mission? To stop the worldwide Emergency, which has the masses living in a state of crippling anxiety due to a constant onslaught of bad news. The new school is a challenge all its own, including unfriendly classmates, bizarre classes, and a shockingly familiar headmaster, Dr. Curtain. The children must stick together and use their strengths to prevent their expulsion and stop the Emergency. While undercover, Reynie and Sticky join Curtain's elite Messengers and uncover the machine responsible for the Emergency's transmissions – the Whisperer. Mr. Benedict, along with his cohorts Number Two, Rhonda, and Milligan, devise a way to reach the children. As Dr. Curtain gears up for the next phase in his plot – known as the Improvement – Mr. Benedict and his colleagues devise a plan to extract the children, the mission clearly becoming too dangerous to continue. As Constance's sensitivity to the Whisperer comes to a head, the kids realize they're almost out of time, and devise a risky plan to stop Dr. Curtain once and for all. In an epic showdown of wills, the Mysterious Benedict Society finally takes down the Whisperer once and for all and the group rejoices, having saved the world. Mr. Benedict invites the team to his mansion for a final reunion and all is well. Or so it seems for now, as Dr. Curtain and his cronies have managed a daring escape...