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After seeing a newspaper article addressed to children with special gifts, eleven-year old Reynie Muldoon goes to a center where he and many other children take a written test with many strange questions relating to logic, bravery, etc. Do you like television? Reynie replied NO. Though he sometimes enjoyed it, it seemed to irritate him a bit. Then there was, Do you like the radio? Reynie replied NO without waiting. Then there was What is wrong with this statement? Reynie said that it wasn't a statement at all, but a question. A very sneaky question that only he got correct was According to the rules of chess, is this possible? To this, he replied YES. It showed one black pawn moving two steps ahead. His logic was that the white knight hopped over, the black pawn came, and the knight went back. He is the only one in the room to pass this exam, and, after all the other children leave, he is invited to yet another center for more tests.
He goes there the next day, and meets Rhonda Kazembe, a distressed girl who lost her only pencil for the test, down the drain. She appears to have green hair and a poofy dress. Reynie offers to help her and Rhonda makes him enter it. He doesn't see a pencil anywhere, and feels scared. After what seemed like forever, Rhonda finally lets him out. Reynie breaks his pencil in half to give Rhonda to use. She says not to worry and pulls out an extra pencil for herself. Rhonda offers him the answers to the test they're about to take. Reynie refuses this, and walks into the testing area. There, he and many other children sit in separated desks, each getting a test. All of the test questions are impossibly hard Reynie notices, some of the other children even start to cry. But Reynie realizes that each of the question's answers have questions in different part of the tests that give the answers. 1-20, 2-21. up to 40 questions. Reynie realizes it is all just a big puzzle.
Because of the logic and skill he showed, Reynie together with three other children named George "Sticky" Washington, a boy with photographic memory, Kate Wetherall, a resourceful and agile girl, and Constance Contraire, a stubborn little girl who likes to recite couplets, is later invited to the home of Mr. Nicholas Benedict, who presents them all with a task to do. He tells them that by using subliminal messaging hidden in television a man named as the "Sender" can make people believe such things. One example of a hidden message is "The missing aren't missing, they've only departed". Benedict tells them that the one sending these messages is a Mr. Curtain, the principal of L.I.V.E. institute: a school on an island off the coast of their city of Stonetown.
Inside the Institute the children see strange people. The lessons are otherwise repetitive.Communicating with Mr. Benedict via Morse Code, the children uncover the hideous plan of Mr. Curtain, to control the people of the world and imprison his enemies.
The children manage to stall Mr. Curtain's plan, allowing Mr. Benedict to shut down the Whisperer, Mr. Curtain's machine which allows him to transmit the hidden messages. Though Mr. Curtain is still at large, the children share a party together with Constance, who is celebrating her birthday.
- Reynard "Reynie" Muldoon is an eleven-year-old living at Stonetown Orphanage. He is extraordinarily good at problem solving, logical deduction, and reading people, and his brains have resulted in the assignment of a special tutor, Miss Perumal, to him. Reynie looks between the lines, observing and questioning, and gets past most obstacles by finding the "puzzle" within the situation. He is described as an especially average-looking boy with average brown hair, average pale complexion, and average clothes.
- George "Sticky" Washington is a dark-skinned boy with a bald head. He is also eleven. He has a prodigious photographic memory and a talent for speed-reading. He is, however, timid and nervous and resorts to polishing his glasses in stressful situations. He ran away from his parents because they forced him into academic competitions and because he later had reason to think that they no longer wanted him around at all.
- Kate "The Great Kate Weather Machine" Wetherall is a twelve-year-old girl who is resourceful and athletic, possessing extreme agility skills and dexterity bordering on the superhuman. She has fair hair and skin. She carries a bucket containing various items, including a Swiss Army knife, a flashlight, a pen light, a bottle of extra-strength glue, rope, a bag of marbles, a slingshot, a spool of clear fishing twine, one pencil and eraser, a horseshoe magnet and a spyglass disguised as a kaleidoscope. She is very cheerful and optimistic. Kate's mother died when she was a baby, and she believes that her father abandoned her. Later on, she joined a circus. However, towards the end of the story, it is revealed that Milligan, whose memory had been destroyed by the evil Mr. Curtain, is Kate's long-lost father.
- Constance "Connie Girl" Contraire is a small, extremely intelligent and precocious, but also extremely stubborn and often unpleasant girl. She has the ability to write clever and whimsical poems, and her ultra-sensitive mind is also the most severely affected by the hidden messages transmitted by the Whisperer. She is shown at the end of the book to be 2, but she still argues, insisting that "I am almost three."
- Ledroptha Curtain is the antagonist of the story and the head of the Learning Institute for the Very Enlightened (L.I.V.E.). Mr. Curtain created the Whisperer and other inventions in order to brainwash all the world's minds, as part of a scheme in which he will control the world and be declared "Minister And Secretary of all The Earth's Regions" (M.A.S.T.E.R.) Partway through the story, he is revealed to be Mr. Benedict's twin brother. He uses a modified wheelchair to get around, due to his narcolepsy, a condition he shares with his brother. However, unlike his brother, his narcolepsy is triggered by anger, whereas Mr. Benedict's narcolepsy is triggered by happiness and laughing.
- Mr. Benedict is the person who started the whole thing. He is the one who wishes to stop Ledroptha Curtain's Whisperer. He has narcolepsy like his twin which is triggered by him feeling strong emotion. He is very reluctant to let the children go on a dangerous mission, but when reminded there is no other way, he allows them to go. He leaves a note to the reader at the end of the book saying that to find his first name, it would be easy if you are acquainted with the code and then the answer lies within your grasp. The key word in the note to the Reader is "code" and the phrase "answer lies within your grasp." In hardback versions of the book, a Morse Code sequence appears on the inside of the book jacket underneath the author's name and blurb, literally where a typical reader would be holding the book. In paperback versions, there is a Morse Code sequence on the back cover of the book, underneath the plot description. His real name is Nicholas Benedict.
- S.Q. Pedalian An Executive working for Mr. Curtain. He is known to be a klutz, but even though he is clumsy, he happens to be the only Executive who is kind to the Mysterious Benedict Society. However, he is somewhat oblivious to the dangerous effects L.I.V.E and the Whisperer have on the world's inhabitants. The author is prone to word play throughout the novel including using locations like Nomansan Island (which could be read as: No Man's an Island, a literary reference to the John Donne statement which also has thematic reference to Reynie's problems in the novel), the careful reader should be aware of the literary reference of S.Q.'s name and his character (including his stated shoe size of 15) to the word sesquipedalian, which translates from Latin as "a foot and a half long."
- Jackson A Head Executive who is unkind, rude, and cruel.
- Jillson A Head Executive with an "I am better than you" attitude. Her reputation is like twin Jackson's, as she is rude, mean, and cruel.
- Martina Crowe is a teenager with long black hair. She is a Messenger at the Institute first, but later on is promoted to the position of Executive by Mr. Curtain even though he does not trust her much. She despises the members of the Mysterious Benedict Society because Sticky and Reynie got better grades than she did, threatening her position as Messenger (since there is a limited number.) She also dislikes Kate because Kate stands up to her and is not afraid of her.
- Milligan is the guard for the children when they enter L.I.V.E and for Rhonda, Number Two, and Mr. Benedict. He is a sad and somber man, even described as a "scarecrow" owing to his shabby and depressing demeanor. His sadness is attributed to his kidnapping by secret agents working for Mr. Curtain, after which he lost all of his past memories, due to the Whisperer. At the end of Book 1, the author reveals that he is the long-lost father of Kate Wetherall.
- Number Two Is one of Mr. Benedict's assistants. She is always referred to by her code name, despite Mr. Benedict telling her that her real name is fine. (Readers do not discover her real name in this book.) She is said to have a 'pencil like' appearance, (which is also a pun on the common yellow #2 pencil) complete with a yellow complexion, rusty red hair, and yellow clothes. She passed Mr. Benedict's tests several years ago, and was later adopted by Mr. Benedict. In the third book you discover her name at the end. She almost never sleeps which results in her eating more than normal people.
- Rhonda Kazembe Is also a former student, but was adopted by Mr. Benedict just like Number Two. She poses as a student during Mr. Benedict's tests, and offers the answers to any child who will take them. If they agreed to cheat however, they would not pass the quiz.
- Miss Perumal She is Reynie's tutor, of Indian extraction, and is intelligent and friendly. She was the only person who was kind to Reynie at the orphanage, and adopts Reynie at the end of the story. She also spoke Tamil, which she was teaching Reynie during their lessons.
- Mr. Rutger is the Stonetown Orphanage director. Blinded by greed, he wouldn't let any children in the orphanage go to an advanced school in order to retain funding he received per child who remained with him.
Two sequels (the second and third books in the series) were published in 2008 and 2009: The Mysterious Benedict Society and the Perilous Journey and The Mysterious Benedict Society and the Prisoner's Dilemma.