The novel A Wrinkle in Time speaks of a battle between both good and evil. The children in the novel, Meg and Charles, are in a battle to save the universe from evil. This evil is named as It or the Thing (Dark Thing). Therefore, given the children represent the good in the world, their antagonist (or foe) is evil and represented by a giant cloud which engulfs all things.
Ultimately, it is up to the children to save the universe from the complete control of the Thing--which means to shadow the world in complete and utter darkness. This would mean that evil had won over good and that darkness proved to be the most powerful entity in the universe.
a more simple way to tell you the answer than the one above me is that the dark thing represents evil.