Most of the human behaviors are executed automatically under familiar circumstances. These behaviors are prepotent in that they take precedence over any other potential alternatives. Yet, humans are also capable of engaging cognitive resources to inhibit such a prepotent behavior and replace it with an alternative controlled behavior in response to an unforeseen situation. This remarkable capability to switch behaviors in a short period of time is the hallmark of executive functions. In this article, we first argue that the prepotent automaticity could emerge at least in three different domains – innate, habitual and motivational. We then review neurophysiological findings on how the brain might realize its switching functions in each domain, primarily by focusing on the monkey oculomotor system as the experimental model. Emerging evidence now suggests that multiple neuronal populations in the shared cortico-basal ganglia network contribute to overriding prepotent eye movement, be its origin innate, habitual or motivational. This consideration suggests the general versatility of the cortico-basal ganglia network as the neural mechanism whereby humans and other animals keep themselves from becoming subservient to reflex, habit and motivational impulses.