Theories of brain function have evolved through multiple stages. The first proposition was that brain networks support a set of reflex responses, with current sensory inputs producing immediate motor outputs. The behaviorist paradigm suggested that actions can always be explained as a response to immediate external cues. In response to these views, the cognitive paradigm argued that behavior cannot be understood simply as input–output functions because the hidden layers of brain generate unpredictability. The central processing was termed “cognition.” Here we propose a neuroscience-based model of cognition. Our core hypothesis is that cognition depends on internal models of the animal and its world, where internally generated sequences can serve to perform “what if” scenarios and anticipate the possible consequences of alternative actions without actually testing them, and aid in the decisions of overt actions. We support our hypotheses by several examples of recent experimental findings and show how externally guided cell assembly sequences become internalized to support cognitive functions.