A Wind in the Door, by Madeline L'Engle, 1973

Meg's 6-year old genius brother Charles Wallace needs rescuing again, but not from the fascist/communist villians on Camazotz -- this time, he needs saving from his own mitochondria, where evil’s seeping influence is corrupting the young and vital farandolae. It's up t0 Meg, a feathery many-eyed cherubim, Calvin, and dour, officey elementary principal Mr. Jenkins, to help him. Theology in humanist clothing, a fantasy sequel to A Wrinkle in Time that does not live up to the first novel's promise, and feels much more overtly philophical and religious. Borrows heavily from the science fiction of C.S. Lewis, particularly his Perelandra trilogy.