It is by now a well-supported hypothesis in cognitive neuroscience that there exists a functional network for the moral appraisal of situations. However, there is a surprising disagreement amongst researchers about the significance of this network for moral actions, decisions, and behavior. Some researchers suggest that we should “uncover those ethics [that are “built into our brains”], identify them, and live more fully by them,” while others claim that we should often do the opposite, viewing the cognitive neuroscience of morality more like a science of pathology. To analyze and evaluate the disagreement, this paper will investigate some of its possible sources. These may include theoretical confusions about levels of explanation in cognitive science, or different senses of ‘morality’ that researchers are looking to explain. Other causes of the debate may come from empirical assumptions about how possible or preferable it is to separate intuitive moral appraisal from moral decisions. Although we will tentatively favor the ‘Set Aside’ approach, the questions outlined here are open areas of ongoing research, and this paper will be confined to outlining the position space of the debate rather than definitively resolving it.