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A step-by-step guide on how to develop a Transformative Theory of Change, for innovation projects, programmes and organisations working on systems transformation. The MOTION project was initiated with one key question in mind: how can we help projects and organisations be more transformative, using the framework and concept provided by the multi-level perspective? And what kind of tools, methods and frameworks can we co-design that translate scientific concepts into practises relevant for policy practitioners? This led us into a co-creation journey during which researchers from the Transformative Innovation Policy Consortium (TIPC) and EIT Climate-KIC project partners experimented, reflected and learned from each other in building the approach that we share in this handbook. Through this journey, we gained a deeper understanding of what the portfolio approach means in a transformative system change context and which skills and competences are needed to facilitate processes of co-creation in the science-policy-practice interface. We had the opportunity to configure the key building blocks of our theoretical approach, the Transformative Outcomes, into practical insights and actions that can easily be applied by innovation organisations at many levels. This handbook is the culmination of the journey as it translates key learnings from the MOTION project into practical insights that are relevant to practitioners working on systems transformation.