A good therapeutic alliance has been found to be the best predictor of outcome in psychotherapy, but psychotherapists also need to develop an understanding of the mechanisms by which that alliance is created and the factors that may damage that alliance and contribute to harmful effects of psychotherapy. I explore these factors in three contexts: the nature of the therapy itself, the characteristics of the therapist, and the dynamics of the patient-therapist relationship. I discuss the research that suggests that potentially harmful processes can be avoided by a dynamic-agentive systems model, which views psychotherapy as a conversation, in which turn-taking, rupture and repair, and perspective-taking are the intersubjective tools that help to build the therapeutic alliance and that can be the focus for further study into the mechanisms by which psychotherapy is helpful or harmful. The neuroscience research that supports this model is summarized.