The novel A Wrinkle in Time is the epitome of a "good vs. evil" story. The theme of the novel is that evil is an active, constant, present force that is consuming worlds and dimensions. This is on prominent display when the three witches show the children the Earth from a great distance, wrapped in a dark shroud with occasional bursts of light illuminating its surface. This represented the lives and actions of good and pure people.
At the climax of the novel, Charles Wallace does mentally battle with a physical manifestation of evil, the disembodied brain IT, eventually winning out because of his love for Meg and their father.
The primary theme in this novel is that there is a true and constant battle between good and evil, and the only way to combat it is through good and charitable loving actions for humanity.