Transformative conceptual learning is key to gaining disciplinary knowledge and expertise but can be troublesome for students. Since 2004, the explanatory Threshold Concept Framework (TCF) has successfully improved student outcomes by identifying and targeting these troublesome transformative concepts with pedagogical support. Recent TCF research has focused on the ‘liminal space’, the time-space where students struggle to grasp transformative concepts. However, no research has fully mapped this learning journey to transformation considering the contribution of critical thinking to this cognitive process. A qualitative approach was used to investigate how critical thinking acts within the liminal space during conceptual learning in undergraduate medicine. Experts and students at an Australian university medical school were interviewed about their experiences of threshold concepts in learning and teaching evidence-based practice and medical biostatistics. This led to a year-long case-study series of students from across the medicine program. Participants were invited to keep a reflective journal of the critical thinking employed at troublesome conceptual learning moments. Journal and interview data were analysed using an abductive analysis method that applied a combined theoretical framework of the TCF and Vygotskian educational development theory. This Vygotskian exploration of transformative learning episodes revealed three main intersections: conceptual learning as a system; language and thinking; and the zone of proximal development (ZPD) and liminal space. Iterative analysis revealed that students experience challenging learning thresholds where individualised conceptual systematisation creates distinct disciplinary conceptual elements. Assimilation of key overarching concepts initiates a core transformation of knowledge and disciplinary perspectives, leading to new ways of thinking and practising with augmented clinical expertise. Most interestingly, language acts as the central cognitive bridge that initiates and enables critical thinking within the ZPD/liminal space. Dialogue with experts and peers was important for student learning, but self-teaching, as inner speech, was significant in exploiting crucial critical thinking steps that unlock transformation. Recommendations are made to emphasise and nurture this intrinsic language-critical thinking integrator system to enhance student conceptual metamorphosis towards medical practitioner identity.