Young Adult Literature; Mystery
Like most young adult lit, The Mysterious Benedict Society has a young adult protagonist (check) who's dealing with issues of identity (check) while trying to navigate his way between childhood and adulthood (check). Sure Reynie's on the young side of the young adult continuum, but he's confronting evil at the Learning Institute for the Very Enlightened (which is EVIL—backwards), so he's definitely getting ready to cross the bridge from childhood to… well, whatever comes next. And there's one last YA box to check off for The MBS: it has a hopeful ending. (Check.)
As for what makes The MBS a mystery, well, it's chock full of clues. From the questions on Mr. B's tests, many of which you can try to figure out along with the characters, to Mr. Curtain's sinister plot, to the hints at Milligan's true identity, Trenton Lee Stewart is continually dropping breadcrumbs for us to follow.
If you didn't pick up on the clues about Milligan, go back and reread his initial description. He has "a weatherbeaten jacket, weatherbeaten trousers, and weatherbeaten boots" (3.4). Gee… Weatherbeaten, beaten weather, Wetherall… see what we mean? We also find out right away that he has ocean-blue eyes (Kate's are bright, watery blue) and hair yellow as flax (Kate's is golden-blond).
And when Kate tells the story of her father, she mentions making him promise they'll go back to the mill, a link that is hinted at by both Milligan's name and Mr. Curtain's journal entry explaining that a relapse of memory can be triggered by the last important thing a person remembers, such as an unfulfilled obligation.
But the mystery of Milligan is just one of the mysteries you have a chance to solve in this book. There's also a ton of wordplay (think about S.Q. Pedalian and then look up the word sesquipedalian; or contemplate Ledroptha Curtain and the phrase let drop the curtain) and plenty of hints concerning the role Constance might eventually play on the team. As well as her real age. So the MBS is a mystery even though we know who the bad guy is all along—it's just that instead of trying to figure out who, you have to figure out what, when, where, why, and how.