A rationale for an intersubjective research paradigm is offered, arguing that this must provide information relevant to understanding an effective psychotherapy process. An example is given of a project where both patient and therapist make ratings reflecting changes in their self-experience during a therapy session, with concurrent measures of breathing and heart rate. Heart Rate Variability (HRV) and breathing are considered with reference to their relevance as markers of autonomic state, with likely variability in relation to feeling states. The frequencies of self-experience ratings are demonstrated to relate to the timings of the present moment and the narrative unit, suggesting that self-states accessible to reflection do not correspond to minimal conscious states. Psychotherapy process is considered in relation to a therapy where the patient begins from a relatively alienated position but undergoes transformations that relate to recognition and protection of the vulnerable self. Tentative connections are made between the experience of self, as reported in ratings, and the physiological, autonomic state, with reference to the Polyvagal Theory.