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.

After narrowly avoiding capture by the imposturous water polo team, the kids try to stay hidden, but are distracted by an underground casino. At Curtain’s compound, an acolyte is found completely unresponsive, suggesting a frightening symptom of his methodology, while Number Two works on an intricate escape plan.

When the kids discover that Mr. Benedict and Number Two have been kidnapped, they must piece together the riddles and clues within a perilous scavenger hunt set by Mr. Benedict to foil Curtain’s latest scheme.

The kids call in the help of an old friend as they scour the countryside for clues to Constance’s whereabouts. Meanwhile, Constance finds herself imprisoned by a surprising foe who hopes to shed light on an old failure.

Heading to the train station, the kids realize that Curtain must have sent multiple teams after them. Benedict, in his state of involuntary elation, praises Curtain for his discovery.

After learning the location of Dr. Curtain’s compound, the Society prepares to strike but is beset by Greys and must split up to escape. Meanwhile, Mr. Benedict tries to bond with his twin in an effort to gain intel, but is sidelined as Dr. Curtain sows discord between Mr. Benedict and Number Two.

Stowaways aboard a majestic ship, the kids try to blend in and find the next clue. Rhonda, Milligan, and Ms. Perumal board a dirigible to catch up to them. Mr. Benedict and Number Two do not hide their distrust from Curtain, despite his attempts to calm them. After observing the unnervingly joyful behavior of his devotees, they figure out that Curtain is using neurological techniques to create artificial happiness. Back at sea, the water polo team sneaks suspiciously towards the kids’ stateroom…

Mr. Benedict and Number Two’s plan to subdue Dr. Curtain backfires. After arriving at the compound, The Society regroups to rescue their captured comrades. Meanwhile, Dr. Curtain hosts a celebration to announce his plans for global expansion.

Freshly arrived at a haven from Number Two's past, The Society bands together to stave off disaster.

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.

The children make a risky play to search for clues right under Dr. Curtain’s nose. Mr. Benedict and Milligan head out into rugged terrain to do some recon of their own. Rhonda and Number Two butt heads about their unique approaches to fighting The Emergency. Sticky gets caught trying to help Kate cheat, and finds out the next phase of Dr. Curtain’s insidious plot. Kate suffers a blow to her academic standing but finds a saving grace in Martina Crowe and her tetherball team.

Reynie and Sticky investigate secret transmissions. Constance and Kate explore the island.

Mr. Benedict reveals the truth about his past with Dr. Curtain – and how he may be partly to blame for Curtain’s misdeeds. The adults agree the mission has gotten too dangerous to continue. Sticky is given a special task during Messenger duty and begins to question his loyalties. Kate and Reynie develop their respective friendships with Martina and Curtain’s son, SQ, and use them to advance the mission.

Kate embarks on a rogue mission into Dr. Curtain’s secret lab which ends in disaster. Mr. Benedict, Number Two, and Rhonda decide to take matters into their own hands. Reynie accuses Sticky of being taken in by Dr. Curtain’s charismatic ways, while Kate’s deception makes Martina a target. Reynie is called into Dr. Curtain’s office for interrogation. Constance’s unique sensitivity to the Whisperer comes to a head, and the team realizes that their time is running out.

Mr. Benedict, Rhonda, and Number Two arrive at The Institute, ready to take down Dr. Curtain and his minions. The kids form an elaborate plan to destroy the Whisperer once and for all. Milligan’s shocking connection to Dr. Curtain is revealed. Dr. Curtain prepares to take an aggressive step forward in The Improvement. The kids, Benedict’s team, and Dr. Curtain face off in a climactic final showdown, the fate of society itself hanging in the balance.

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.