Why does God let bad things happen? Why did God let some jerk break into my home and violate my sense of safety? Easy. Because that jerk has free will.
Because free will is such a great explanation, people who think about the problem of evil have identified a subset of the problem of evil called the natural problem of evil. In other words, why did God let a meteorite crash through my roof and ruin my only home? The meteorite doesn’t have free will.*
Free will can still explain the natural problem of evil. First, consider what God’s respect for man’s agency implies. It implies that he values human choice and would want more of it. It implies that he particularly values *meaningful* human choice, i.e., informed choice that has real consequences. (1) Natural evils help inform choices by showing us what pain and suffering and evil are. This is Eve’s theodicy in the Pearl of Great Price. (2) Natural evils also inform choice because they arise from natural laws and an ordered universe. The hurricane happens because the laws of physics are what they are. But if the universe were not orderly and law-bound, humans would have a much harder time in principle predicting the consequences of their choice. (3) Natural evils also increase the scope for human choice and increase the possible range of consequences. The possibility of hurricanes make choices about the kind of house I build have a greater range of consequences and therefore be more meaningful. Hurricanes means I have meaningful choices to make about disaster relief and charity even if I live far from the coasts. At the very largest scale, hurricanes and other natural disasters mean collective choices made hundreds of years ago that may have delayed or advanced science and technology, or cultural resilience and charity, still have meaningful consequences today.
We mortals aren’t the only ones whose free will is wrapped up in natural evils. The devil and his court have agency to act within bounds, and not just to act on the human will. I firmly believe that some natural evils and perhaps even the whole fallen condition of the natural world are the result of diabolic manipulation of chaotic natural variables.
Finally, I firmly believe that angels are set as monitors and managers of much of the natural world. And angels are imperfect beings. I would even argue that angels are probably capable of some degree of sin. Dan Peterson writes about this idea today.
*Some Mormons would say that it does, in a way, but that doesn’t solve the natural problem of evil. Mormons who believe that every created thing is a conscious agent also believe that of all creation only Man uses its will to disobey God. So while we can say of human free will that God didn’t want you to choose what you chose, we couldn’t say that of other created things.