Conditioning, extinction, and reinstatement are fundamental learning processes of animal adaptation, also strongly involved in human pathologies such as post-traumatic stress disorder, anxiety, depression, and dependencies. Cued fear conditioning, extinction, restatement, and systematic manipulations of the underlying brain amygdala and medial prefrontal cortex, represent key experimental paradigms to study such processes. Numerous empirical studies have revealed several aspects and the neural systems and plasticity underlying them, but at the moment we lack a comprehensive view. Here we propose a computational model based on firing rate leaky units that contributes to such integration by accounting for 25 different experiments on fear conditioning, extinction, and restatement, on the basis of a single neural architecture having a structure and plasticity grounded in known brain biology. This allows the model to furnish three novel contributions to understand these open issues: (a) the functioning of the central and lateral amygdala system supporting conditioning; (b) the role played by the endocannabinoids system in within- and between-session extinction; (c) the formation of three important types of neurons underlying fear processing, namely fear, extinction, and persistent neurons. The model integration of the results on fear conditioning goes substantially beyond what was done in previous models.