Clearly, methodological naturalism will fail if it attempts to explain a phenomenon that is not completely naturalistic. For instance, imagine that human consciousness and will amount to more than mere atoms in motion. Perhaps, for example, there is a soul that transcends the material world. Then science's attempts to explain our thinking will rule out the right answer if science is constrained to methodological naturalism. Methodological naturalism would be wrong, and the question is: how should we handle such cases if they are encountered?
I can only think of four possible answers to this question, so this amounts to a simple multiple choice option:
A. Don't worry, methodological naturalism never fails because nature is always fully materialistic.
B. If methodological naturalism ever fails then science, constrained to methodological naturalism, will lead to the wrong answer. Don't worry, it is fine if science is sometimes incorrect.
C. If methodological naturalism ever fails then science should back away from the problem at hand. Science should only address phenomenon that are fully naturalistic.
D. Science should not be constrained to methodological naturalism.
It seems that while evolutionists routinely mandate methodological naturalism, they just as often fail to explain just what they mean. In fact, I know of no such evolutionist who has answered this question. So here is a simple multiple choice. All we need is a simple "A", "B", "C" or "D".