Recent critiques of methodological naturalism (MN) claim that it fails by conflicting with Christian belief and being insufficiently humble. We defend MN by tracing the real history of the debate, contending that the story as it’s usually told is mythic. We show how MN works in practice, including among real scientists. The debate is a red herring. It only appears problematic because of confusion among its opponents about how scientists respond to experimental anomalies. We conclude by introducing our preferred approach, Science-Engaged Theology.