Propagandizing
The centerpiece of the plot of this novel involves the transmissions of secret messages via and radio and TV transmissions. These messages ultimately effectively wipe away actual memories and instill ideas into the minds of listeners. The effect is similar to subliminal messaging placed within things like music or advertising, but that is primarily for the purpose of plot mechanics. On a thematic level, the secret messaging being put out using the device known as the Whisperer is actually more akin to the music or advertising itself. The thematic exploration of this idea of secret messages being sent out to change people through manipulation is social commentary on the impact of mass communication as propaganda.
Being Gifted
The titular organization known as the Benedict Society is comprised of children: Reynie Muldoon, George "Sticky" Washington, Kate Wetherall, and Constance Contraire. Each of these children is gifted with some special ability. After answering an ad seeking specially gifted children, each are administered and pass a test which results in them being chose by the mysterious Mr. Benedict to save the world from the manipulative propagandizing of the secret messages being sent out Mr. Curtain through a device known as the Whisperer. This story becomes one of many which are thematically connected by the repetitive narrative trope of the special abilities of gifted children being manipulated by powerful adults for their own purposes. The kids that make up the Mysterious Benedict Society are not treated as individuals whose "gifts" are nurtured for the purpose of individual expression but rather are just components for one powerful adult to defeat another powerful adult.
The Power of Fear
The primary motivating factor in the secret messages that Mr. Curtain employs in his attempt to gain control over the masses is fear. Reynie even reminds his fellow society members that Mr. Curtain believes "fear is the most important element in human personality." This theme is explored not just from the perspective of fear naturally being an ally of those seeking power. The theme is intensified through the additional resonance of how one can gain power by playing upon people's fears by actually creating new things to scare them. The creation of unfounded and even irrational fears resonates strongly within the post-truth zeitgeist of "alternative facts" and mass acceptance of disproven conspiracy theories.
