How can one reconcile God being the One who sends down rain and thunder with modern scientific explanations for natural phenomena such as rainfall, thunder, lightning, the formation of mountains, earthquakes, and volcanoes, especially since modern science proves that the Earth was formed gradually and through the movement of tectonic plates?

There is no contradiction between what modern science has revealed regarding the causes of natural phenomena and the fact that these phenomena are in the hands of God, who disposes of them as He wills. God created these phenomena and their causes. What modern science uncovers are the causes that God made and linked to their effects. It must be noted that not everything stated by modern science is definitive, as many scientific theories are conjectural and subject to change. The gradual formation of the Earth does not contradict religion; for His saying, "Indeed, your Lord is Allah, who created the heavens and the earth in six days and then established Himself above the Throne" [Al-A'raf: 54], could mean that the days are like our days, or not. A day with Allah is like a thousand years of what we count. If the implication of the verse contradicts the gradual creation of the Earth, then what came with the revelation is correct.