Methodological naturalism is usually understood to be the idea that a subject will be investigated as if supernatural causes do not exist. This is often considered to be a part of science, and therefore theories such as intelligent design cannot be scientific. While intelligent design theory is not a scientific theory, this issue should still be resolved in order to better understand the place and necessity of methodological naturalism.
Science deals with the powers, dispositions, structure and composition of natural things. Science is the study of a thing according to the kind of thing it is. It does not deal with particular things as particulars. History, on the other hand, deals with particular things as particulars. For this reason, history deals with the past of particulars and their relationships to other particulars. Most history departments only deal with written human history. However, prehistory (meaning prior to written history), paleontology and historical science are all forms of history. Because the basic data of these disciplines is found by scientific research or tools, many of the researchers are scientists. It is not surprising that many of these scientists think of their work as scientific rather than historical.
But there are some key differences between scientific work and historical work. The first difference is that historical study is a matter of probability. Any and all historical theories are supported by evidence that is not deductive in nature. We might consider them to be inferences to the best explanation, or Bayesian probabilities but they cannot be deductions. The second difference is a result of the first one. Any historical theory may be replaced by a theory that completely rejects the central points of the first theory. It might be unlikely, but such a thing is always possible. Third, historical theories are not based on experiments, repeatable or otherwise nor are historical theories subject to empirical verification. The evidence for a historical theory may be empirical, but the theory itself is not. These differences mean that one cannot simply treat science and history as similar disciplines.
Methodological naturalism is necessary in science because science requires that as a precondition of investigating natural things. Suppose someone claimed that gravity was an act of God. Such a thing might be true (in some Eastern religion perhaps), but if science is to investigate gravity, it must assume that gravity is not an act of God. First, there is no possible way to rule out of the act of God hypothesis. In this way, it is much like supposing that our entire lives are illusions, that the universe is irrational in its foundations or that natural things have nothing in common with each other. Each of these things are simply assumed to be false by the mere act of scientific investigation. This is the second reason. The mere act of scientific investigation supposes that we can understand, investigate and empirically determine what the causes of something are. But we cannot do this with acts of God. Therefore, methodological naturalism is both unavoidable and necessary for science.
Methodological naturalism is not necessary for history. History does not investigate by empirically determining anything. Although history does seek to answer questions about the past, it requires only that the past be rational. Rational simply means that there is a reason. So if something did happen that were an act of God in the past, then as long as that act had a reason, history can investigate it. Hume’ s arguments against miracles are an abject failure. Much of the modern animus against miracles is motivated by those reasons. Therefore, moderns have no good reason to reject miracles as such. Each miraculous case must be taken on its own merits and the evidence considered individually. Having said that, miracles cannot be a common occurrence in history. Their occurrence has to be low enough that they do not alter science research. That is fairly easy though, miracles must be less common than one part in five enough to lose statistical significance.
This result means that miracles cannot be removed entirely from consideration in the historical sciences. They are a division of history rather than science, and what applies to history in general applies to them. However, evidence must be found to support them in particular cases. While this is not directly relevant to intelligent design theory, it does affect creationism. Since many intelligent design theorists are also creationists, this is an argument that they advance as creationists. (It is possible to believe in intelligent design theory and claim that aliens are responsible for the features that were caused by an intelligence.)