Sovereignty: God is the ultimate cause of everything that happens in the universe (which includes angels, humans, animals, plants, rocks, and all else). It is His creation. But this does not imply that nature is merely a reflection of the essence of God, or that evil in the world is caused by God. That is an exaggeration.
On the contrary, history is real, including the moral decisions of individuals.
But this does not imply the exaggeration: that creatures are autonomous.
Providence and Sovereignty: So Christian doctrine acknowledges God as the sovereign ruler over all things, but on the other hand, the human nature that God created is real, including moral choices of individuals.
There are two mysteries combined in this dilogic: the mystery of time, and the mystery of evil. We cannot fully comprehend either of these, because we are temporal and we are sinners. In dealing with this subject, "we see through a glass darkly" (I Cor. 13:12).