The third installment in the Mysterious Benedict Society series opens in Stonetown, where four gifted children have been living for months under government-ordered protection in the old house of Mr. Benedict, a brilliant, kind man who has narcolepsy. The children and their families are confined because of the ongoing threat posed by Mr. Benedict's twin brother, Ledroptha Curtain, a ruthless fugitive determined to reclaim his invention, the Whisperer: a chair-like device with a red helmet, capable of suppressing or retrieving memories and reading minds. The Whisperer is locked in a third-floor chamber and powered remotely by tidal turbines Mr. Curtain invented in Stonetown Bay.
The four children, who privately call themselves the Mysterious Benedict Society, are Reynie Muldoon, a twelve-year-old with exceptional problem-solving skills; Sticky Washington, a boy with a photographic memory; Kate Wetherall, a physically gifted girl who carries a red bucket of useful tools; and Constance Contraire, a stubborn four-year-old with emerging telepathic abilities. The story begins with a lesson based on the Prisoner's Dilemma, a game theory exercise about cooperation and betrayal. Rather than choosing between the given options, the children trick their instructor, Rhonda Kazembe, Mr. Benedict's adopted daughter, and escape the room together. Mr. Benedict is amused but reminds them that actions have consequences for others.
Life under confinement has grown tedious. The children cannot attend school, leave the property, or join the adults on periodic errand days, when the household ventures into Stonetown through a secret tunnel escorted by Kate's father, Milligan, a top secret agent. Reynie notices that a guard named Mr. Bane is suspiciously never on duty during errand day, but Mr. Benedict says only that it would be "imprudent to speak of it further" (42). A government official named Mr. Gaines demands that Mr. Benedict use the Whisperer on Mr. Curtain's captured associates to extract intelligence, but Mr. Benedict refuses. The children eavesdrop and learn that Mr. Gaines intends to remove the Whisperer, and that Mr. Benedict has been researching whether the device could alleviate his narcolepsy. Ms. Argent, another official at the meeting, notes this research could benefit millions.
Mr. Benedict gives the children a riddle whose answer is "love," hinting at why Mr. Curtain keeps S.Q. Pedalian, his least competent but most loyal assistant, close. During exercises testing Constance's abilities, she transmits thoughts into Reynie's mind and, more alarmingly, mentally forces Sticky to believe he dislikes vanilla ice cream. The effort leaves her violently ill, and Mr. Benedict warns her never to attempt such a thing again.
Events accelerate when Mr. Pressius, a wealthy businessman secretly working with Mr. Curtain, arrives claiming to be Constance's father with forged documents. Mr. Benedict assures Constance it is a ploy to distract him before the Whisperer's scheduled removal. Desperate to learn the truth, Constance insists Mr. Benedict use the Whisperer to recover her buried memories. Through the session, she recovers a vivid memory: at barely two years old, she escaped a foster home when Mr. Curtain's agents came to purchase her for her gifted mind, fled with her birth records, and hid in a library for weeks before using self-hypnosis to forget everything traumatic. The records confirm she is an orphan, not Mr. Pressius's daughter.
When Sticky accidentally reveals the library burned down, Constance flees the house in anguish. That evening, the power goes out across Stonetown. Reynie spots Mr. Curtain's Salamander, an armored, amphibious vehicle, gliding down the lane with Ten Men, Mr. Curtain's dangerous henchmen. The children escape to a cellar while the Ten Men steal the Whisperer, leaving burned substitutes to disguise the theft. The children find torn-up instructions left by a careless Ten Man reading "Rendezvous and search Abbot Edifice 2100 hrs" (183), which they decode as the Monk Building at nine o'clock. Kate uses the secret tunnel to spy on the Ten Men and retrieves further instructions containing coded rendezvous details: "In the root / By the mover / To the north / At noon" (220).
Mr. Benedict confirms Mr. Bane is Mr. Curtain's spy, deliberately kept on as the least dangerous option, and explains that Mr. Curtain orchestrated everything to steal the Whisperer. Overcome by exhaustion, Mr. Benedict falls asleep repeatedly. Reynie experiences a mental flash: the sequence "133 N292," a Dewey decimal call number transmitted telepathically by Constance. The children race to the Stonetown Main Library and find her hiding there. They decode the rendezvous instructions using the principle that "opposite" is the key, determining the meeting is at Ferund Square at midnight. Kate goes alone to spy from the nearby Pittfall Building. Too late, Reynie realizes the entire trail of clues was planted to lure them into a trap. McCracken, the Ten Men's leader, captures all four children, who are blindfolded and driven to an abandoned prison complex where Mr. Curtain waits.
S.Q. brings the children food and inadvertently reveals Mr. Curtain's plan to extract classified secrets from government advisers using the Whisperer. Constance transmits their location telepathically to Mr. Benedict, then falls asleep and receives a coded image: Mr. Benedict, Milligan, Rhonda, and Number Two, Mr. Benedict's other adopted daughter, wearing silly disguises and holding S-shaped pies. The children decode the message: Mr. Benedict has intercepted the real spies and is coming disguised as them. They then overhear Mr. Curtain discussing the password system he uses to verify visitors at the gate. Constance tries to warn Mr. Benedict telepathically but senses the rescuers are still approaching. The children escape their room by trapping a guard, then reach Mr. Curtain's work space as McCracken radios that the van has arrived. Constance reads the password question from Mr. Curtain's mind; Sticky supplies the answer, "electromagnetic radiation," and Milligan's team storms the compound.
A chaotic battle erupts. Milligan dispatches several Ten Men and engages McCracken in a fierce rooftop fight but slips off the edge. Kate uses her falcon, Madge, to startle McCracken and seizes his briefcase, but McCracken corners the children in the courtyard. Milligan, having climbed back up by scraping finger-holds in the mortar, throws himself off the roof onto McCracken, knocking the Ten Man unconscious but breaking multiple bones.
Mr. Curtain, who has made the Whisperer portable by attaching its helmet to his wheelchair, confronts the children and demands they serve as hostages. They refuse, and Mr. Curtain summons S.Q. for help. Reynie and the others appeal to S.Q.'s conscience, revealing that Mr. Curtain has been suppressing S.Q.'s memories to keep him loyal. For the first time, S.Q. refuses to obey. Mr. Benedict arrives and steps between his brother and the children. Mr. Curtain attempts to use the Whisperer to erase Mr. Benedict's memories, but the device fails. Mr. Benedict reveals that he programmed a hidden virus that has permanently disabled the machine. Mr. Curtain abandons his wheelchair and tries to flee in the Salamander, but the wheelchair crashes into a construction crane, dislodging a massive suspended beam. S.Q. holds the crane lever to prevent the beam from falling. In a moment of unexpected feeling, Mr. Curtain turns back from the river. S.Q. grabs him and drags them both to safety as the beam crashes down. Mr. Curtain clings to S.Q. while berating him, but Reynie observes that his eyes betray something resembling relief, or even hope.
In the weeks that follow, Mr. Gaines is removed from his post, Ms. Argent is promoted and closes the case, and the Ten Men, Mr. Pressius, and Mr. Bane are taken into custody. Constance's adoption documents are found among salvaged library books, allowing Mr. Benedict to officially adopt her. Constance discovers that Mr. Benedict was hours from completing his narcolepsy cure when he postponed it to help her, and she insists on using her telepathic abilities to replicate the effect. The effort makes her severely ill, but it appears to succeed: Mr. Benedict reads one of Constance's poems aloud and laughs without falling asleep. Milligan retires, and the families settle permanently around Mr. Benedict's house. At a final bittersweet meeting, Reynie reflects that he has never felt so light, having learned he is not solely responsible for everyone. They are all responsible for each other.