The picture of a deterministic universe is difficult to reconcile with the phenomenology of agency, deliberation, and choice. While everyday conceptions of individual freedom and responsibility depend on the pre-theoretical assumption that we have meaningful control over our decisions and volitional actions, if determinism is true, the outcome of any deliberative process is always the only outcome available; the inevitable result of a reasoning sequence that could not have proceeded any other way. However compelling our ordinary sense of agency and control is, determinism gives us reason to doubt that we have the kind of freedom that we intuitively take ourselves to have. The debate over whether free will is compatible with determinism is a long-running one, traditionally motivated by, and entangled in further disputes about what kind of freedom or control is required for moral responsibility. In a promising and refreshing turn, recent work by philosopher of physics, Jennan Ismael, has significantly advanced the debate. Leaving aside questions about moral responsibility, Ismael’s naturalistic account shows that the freedom we ordinarily take ourselves to have is not threatened by deterministic physics; when determinism is understood on its own terms, stripped of imposed notions of compulsion and necessity, the purported tension between freedom and determinism is resolved. Furthermore, Ismael argues, biological systems with the capacity for representational thought have evolved unified, emergent ‘selves’, and the capacity for self-governance, behavioural flexibility and deliberative control. Following Ismael’s methodology of naturalistic pragmatism, I aim to enrich her contextualised picture of human agency with a precise, unified account of the nature of agency itself, and to further develop this integrated account of freedom and the structures that underpin freedom. Building on Ismael’s account of the self-governing free agent, I aim to fill out some of the details of the cognitive structures that underpin our first-person experiences of choice and endogenous control of action, and discuss how those structures arise in the natural order. Using the predictive processing framework to explore the structures of agency, choice, and autonomy that underpin self-governance, I argue that our potential for freedom – freedom in its most fully developed manifestation – lies in our capacity for autonomy, which is realized when we act deliberately to modify our own cognitive processes and transform our own minds.