This thesis examines the inherent conflict between player autonomy and musical structure in video games. Many of the rhythmic and expectation based structures thought to evoke strong emotions in response to music are difficult to achieve given the temporal uncertainties of gameplay, where the player has the autonomy to act at any time. This dichotomy has long been recognized but its implications have not yet been fully articulated or understood, and the lack of an empirically tested solution represents a significant gap in existing knowledge. A range of existing concepts are analysed from a Self-Determination Theory perspective in order to develop a new model of intrinsic and extrinsic motivations for engagement with video games. In analyzing the video game soundtrack through the perspective of this model it is identified that the inability to reconcile player autonomy and musical structure creates a fundamental dissonance between and within the ludic and narrative roles of music in video games. It is argued that much of the current practice within video game development places music in the reactive position of responding to game events, and that a more interactive position involving two-way communication between music and the game system may represent an opportunity to address this seemingly intractable problem. In developing and empirically testing a new integrated design paradigm for reconciling the conflicting nature of player autonomy and musical structures within representational video games, expertise and musicality are identified as critical factors in the analysis of the player experience. A new area of future research, that of isocrony between musical structures and player actions, is identified as a pre-requisite for further understanding these relationships.