The novel’s main theme is the importance of cooperation. Each member of the Mysterious Benedict Society brings with them particular skills and attributes, and when they cooperate and work together, they succeed. It is not readily apparent to the children at the beginning of the story that they are all pieces of a whole that collectively provides all the elements necessary to complete their mission. There is some squabbling at first, particularly between Constance and the others, as their personalities clash and it is not yet clear why they have been brought together. Mr. Benedict must emphasize that each one of them is vital to the team, that they must respect and appreciate what each of them has to offer the group. The truth of this becomes evident at the end of the story, when Constance’s particular strength, her unparalleled stubbornness, is precisely the trait needed to resist the Whisperer and Mr. Curtain.

Through cooperation the team accomplishes more than they could individually. This does not come naturally to the team, as all of them have lived lives of isolation. Reynie and Constance are orphans, Kate believes herself to be an orphan, and Sticky ran away from his parents.