This chapter contains an analysis on innovating science education from a whole system approach at a national level. Despite national strategies and programs, young learners in Denmark opt out of science education. To counteract the current situation, the Danish Academy of Science Education (NAFA) works to spur motivating science teaching across the Danish educational system. A transdisciplinary program of this size and scope has not previously been executed in Denmark. The analysis of the program presents itself as an autoethnographic assessment of this national science program, offering open-ended reflections at an internal operations level, and thus providing an analysis of NAFA as an ecosystem for collaborative innovation of science education in Denmark, and pointing to drivers and barriers for trans-institutional program leadership to facilitate systemic change. The chapter elaborates on central questions that all lead to the build-up of a research conclusion, pointing to the importance of collective leadership sensemaking, boundary spanning and building informal learning communities—activities in favour of anchoring science teaching in local initiatives to spur long term and sustainable macro-scale impact, thus pointing towards the interconnectedness of large scale systems in change efforts. This autoethnographic analysis is an addition to current Scandinavian studies in the area of large-scale innovation of science education.