Thomas Nagel, author of the famous "What Is it Like to Be a Bat?" (1974), fits the description of an atheist who ardently rejects Naturalism (with a capital "N"). For Nagel, a philosopher of mind, the mind cannot be simply reduced to the brain or as a mere emergent property. In support of this, we are reminded that thoughts have a certain aboutness concerning them. Why is this so important?
Well, aboutness cannot be explained in terms of only physical processes. To think about something is to have an intentionality concerning what is thought about. However, where in the brain can aboutness or intentionality be found? Nowhere, at least according to Nagel, as well as many theistic philosophers.
If one were to explore the human brain, sure, there would be neurons firing away. However, neurons aren't about anything; they're simply physical parts of the brain. They might be used to express aboutness, but this is no different than a pianist using a piano to play some beautiful music. While Nagel does not use any modal argument in favor of mind-body dualism (or its cousin, hylomorphism), his argument does help to supplement such arguments:
1. Possibly, my mind exists apart from my body. (Premise)
2. Necessarily, whatever two objects do not possess the same attributes are not identical. (Premise, Leibniz's Law)
3. Therefore, my mind is distinct from my body. (From 1 and 2)
This isn't a theistic argument per se, although philosophers, such as J.P. Moreland, provide further arguments based on this in favor of theism. However, if this is a sound argument, then not only is Naturalism defeated, but the atheist can no longer claim that God's immaterial mind is something contradictory or incoherent.