In his famous essay “Of Miracles,” Hume defines a miracle as a “transgression of a law of nature by a particular volition of the Deity, or by the interposition of some invisible agent.” (C. Stephen Evans and R. Zachary Manis, Philosophy of Religion: Thinking about Faith, 126)
What are miracles? Are they transgressions of scientific laws? Many people especially atheists might think so. Statements might be made even by Christians that miracles involve a "suspension" of the laws of science, or that laws of science are inapplicable for the "special" occurrences when miracles happen. I would suggest however that such explanations are very unhelpful and give the wrong impression to others of how God works in this world.
Christianity is true. Thus, God is a personal being who acts on this world. Normally, he acts via providence, but sometimes he acts via miracles, which are distinct special acts different in kind from providence. The world therefore is always the theater of God's actions. Therefore, from a Christian perspective, the idea of a neutral impersonal world where God interrupts via miracles may be the perspective of skeptics, but it is certainly not the Christian perspective. Here already, we see a different starting point, a different interpretation grid as we attempt to understand miracles.
Next, we have to know what is science. Science is the study of how the world works through what is often term "the scientific method." To simplify things, science normally involves experimentation involving cause and effect to understand and formularize how various forces and processes in the world work. In experimentation, two of three things are present: initial conditions, final conditions, equation of process(es). An experiment or experiments are done (with controls) to figure out the unknown, experiments are repeated where possible, and thus scientific knowledge is gained.It must be noticed that the scientific method must assume methodological naturalism, or that only nature is at work in the scientific processes under study. One cannot assume a demon has tinkered with the scientific experimentation, or science would be undoable.
Putting the two together, science is the study of God's providence. But since miracles are not providence, obviously it is out of the domain of science. It is in that sense correct to say that the laws of science are "inapplicable" for miracles, or that the law of science are "suspended," but such statements are not helpful because they make it seem as if God somehow does away with the laws of science when He does miracles, but that is totally untrue.
When God works, He acts. In miracles, God works differently to create the outcome He desires. Thus, the best way to understand miracles is as an external force working through unknown (supernatural, spiritual) processes to accomplish the end of what God desires. A good way for us to understand such an action is through an analogy in science. Suppose that I add one mole of copper powder to two moles of hydrochloric acid (HCl) in solution. I would get one mole of Copper Chloride (CuCl2) solution, which is a blue solution. But suppose that someone added two moles of Sodium Hydroxide (NaOH) solution to my nice blue solution, without my knowledge. The resulting mixture would be two moles of sodium chloride (NaCl) or common salt in solution with a nice precipitate of one mole of copper hydroxide (Cu(OH)2) at the bottom. Since I did not know of the tinkering done to my solution, what would I see? I would observe that adding copper powder to hydrochloric acid would give me a clear solution of sodium chloride and an insoluble greenish blue precipitate at the bottom. I would most certainly find it strange and suspect that my experiment has been tampered with, since I obviously know what I should be getting.
Miracles can be seen as analogous to the unknown person adding the NaOH solution to the reagent mixture. In miracles, God as a third party acts on the situation on hand, thus the outcome is not what we might have expected. Of course, God not only acts, he acts using divine processes and forces, and therefore the outcome may seem out of this world, but that does not imply a "suspension" of natural laws but rather processes that we do not know and could not qualify. Some miracles are obviously more "miraculous" than others, yet if we understand God as working, God did not transgress the "laws of science" because scientific laws cannot prevent the action of divine forces and processes from changing the outcome. When Jesus turned water into wine, Jesus could have teleported grapes into the containers, do a time acceleration warp, remove the fermented grapes and thus wine is produced.
In the Marvel Cinematic Universe, magic has been seen as advanced science. Miracles of course is not advanced science, but in concept there is nothing to suggest that is could not be miraculous forces causing the change as an external agent, not through breaking the laws of science, much like magic in the MCU are unknown forces causing changes as external agents. If we understand miracles in this manner, which I think is the better way to understand miracles, then we can show how miracles are not contrary to science, just contrary to scientism.