Phenomenological research indicates that disturbance of the basic sense of self may be a core phenotypic marker of schizophrenia spectrum disorders. Basic self-disturbance refers to disruption of the sense of ownership of experience and agency of action and is associated with a variety of anomalous subjective experiences. Little is known about the neurocognitive underpinnings of basic self-disturbance. In these two theoretical papers (of which this is Part 2), we review some recent phenomenological and neurocognitive research and point to a convergence of these approaches around the concept of self-disturbance. Specifically, we propose that subjective anomalies associated with basic self-disturbance may be associated with: 1. source monitoring deficits, which may contribute particularly to disturbances of "ownership" and "mineness" (the phenomenological notion of presence or self-affection) and 2. aberrant salience, and associated disturbances of memory, prediction and attention processes, which may contribute to hyper-reflexivity, disturbed "grip" or "hold" on perceptual and conceptual fields, and disturbances of intuitive social understanding ("common sense"). In this paper (Part 2) we focus on aberrant salience. Part 1 (this issue) addressed source monitoring deficits. Empirical studies are required in a variety of populations in order to test these proposed associations between phenomenological and neurocognitive aspects of self-disturbance in schizophrenia. An integration of findings across the phenomenological and neurocognitive "levels" would represent a significant advance in the understanding of schizophrenia and possibly enhance early identification and intervention strategies.