We argue that phenomenology can be of central and positive importance to the cognitive sciences, and that it can also learn from the empirical research conducted in those sciences. We discuss the project of naturalizing phenomenology and how this can be best accomplished. We provide several examples of how phenomenology and the cognitive sciences can integrate their research. Specifically, we consider issues related to embodied cognition and intersubjectivity. We provide a detailed analysis of issues related to time consciousness, with reference to understanding schizophrenia and the loss of the sense of agency. We offer a positive proposal to address these issues based on a neurobiological dynamic-systems model.