The history between psychoanalysis and the neurosciences has recently been fraught with tension between a complex model of the mind and a biologically reductionistic model of the mind. In the present article, we outline a research model that offers a bridge between the two models by fusing a psychoanalytic approach to mental phenomena with neuroscientific assessment of social cognitive functioning in a sample of patients diagnosed with borderline personality disorder. Specifically, neural activity corresponding to trust appraisal, and rejection sensitivity will be compared with clinically rich ratings of narratives derived from the Object Relations Inventory and Adult Attachment Interview. Our strategy permits an analysis across psychological, behavioral, and neurobiological levels of data in order to better understand the multiple levels of analysis at play that lead to borderline personality disorder. Furthermore, we believe this model could provide a template for neuropsychoanalytic research that preserves psychoanalytic models without reducing them to solely biological processes.