First of all, the storm sets the stage for "a dark and stormy night." Meg's life is stormy, and as she, Calvin, and Charles Wallace face their adventures, they will battle darkness itself.

The cause of the storm as a natural force is the meeting of heat and cold. The temperature differences moves the air molecules in an erratic pattern, seemingly senseless but with deadly purpose. This symbolizes the war between good and evil that will draw in Meg and the others. The juxtaposition of the opposing forces (both in the storm and in the battle) are the result of that clash.

L'Engle possibly could use the storm as representative of the wholeness of the universe, both the physical and the spiritual. What occurs in the spiritual world (good vs. evil) effects the physical world and the humans living in it. The great cosmic battle overflows into the physical realm, setting off the atmospheric disturbance. In chaos, evil excels. In the sequel "A Wind in the Door", L'Engle speaks of echthroi, evil spiritual beings whose existence disturbs the natural world, as well as the spiritual psyche of people. In the case of the storm, we can say that "the echthroi are moving....."