Themes of the book A Wrinkle in Time are:
Love. Love is how they save Charles. Love allows them to save Meg's dad.
Evil vs. Good. An example of this is how the Misses and The Happy Medium explain how world leaders like Gandhi, MLK Jr., and others fought against the black thing.
Being different. Being different is important because Meg is different in that she has no care for school, and Calvin has so little connection to his family.
Adapting to change is important because they have to visit alein worlds struggle through many many things just to save her dad and charles.