The concept of presence is commonly related to whether or not a user feels, acts, and reacts as if he/she were in a real familiar environment when using a virtual reality (VR) application. Understanding the neural correlates of presence may provide a foundation for objective measurements and important constraints for theoretical explanations. Here, we focus on the importance of expectations and their violation in several theoretical descriptions of presence in order to investigate neural correlates of disrupted presence. Functional magnetic resonance imaging (fMRI) was used to measure brain activity during execution of everyday tasks in a naturalistic virtual environment (VE). Time periods with disrupted presence were identified using subject reports of strange situations, interpreted as violations of expectations related to the sense of presence. Disrupted presence was associated with increased activity in the frontopolar cortex (FPC), lateral occipito-temporal cortex (LOTC), the temporal poles (TP), and the posterior superior temporal cortex (pSTC). We relate these areas to integration of key aspects of a presence experience, relating the (changing) situation to management of task and goals (FPC), interpretation of visual input (LOTC), emotional evaluation of the context (TP) and possible interactions (pSTC). These results are consistent with an interpretation of disrupted presence as a re-evaluation of key aspects of a subjective mental reality, updating the synchronization with the virtual environment as previous predictions fail. Such a subjective mental reality may also be related to a self-centered type of mentalization, providing a link to accounts of presence building on the self.