Growing up in 1943 war-torn England, thirteen-year-old Alice and her older sister Louise are members of a centuries-old spy clan, but when Louise decides to spy for the enemy, their bond is changed forever.

Four children complete a series of challenging and creative tasks, and become the Mysterious Benedict Society. After being trained, the four travel to an isolated school where children are being trained by a criminal mastermind to participate in his schemes to take over the world.