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This article continues the project begun in the previous article titled: “The Self as a Complex Adaptive System. Part I: Complexity, Metapsychology, and Developmental Theories” (Palombo, 2013). Using systems theory and a complexity perspective, that article provided a critique of psychoanalytic developmental theories. This contribution addresses some of the methodological issues related to data collection on development and the effects of the observer on the observed. It introduces the Level of Analysis perspective as a heuristic that permits the use of a complexity view applicable to the construct of the self as a complex adaptive system. It proposes three levels, each of which is associated with a platform from which phenomena are observed, a neuropsychological level (L-1), an introspective level (L-2), and an interpersonal level (L-3). The article concludes with a plea for a unifying psychoanalytic paradigm that brings together the data from these three levels and that would lay the groundwork for a clinical theory that would bring together the major existing psychoanalytic theories.