The economy is a complex system, and the interactions between different agents are still not easy to quickly see-through. This complexity should reflect in a spatial dimension; in this way, tracking the tradeoffs opens a new window to the nexus of place and flow. Due to the fact, the economic systems often go through transitions and end up in another state, and this evolution is embedded in cities as the new motor of paradigm shift. To adequately represent and study these dynamics, we aim to develop an integrated method based on network analysis science and geographic economy synthesis to detect a multiscale navigator to track the transition from regional to the local level. This paper seeks to explore the specialization of regional clusters and their innovative behaviour in a particular lagging region, hence unfolding the innovation ecosystem to the smallest granularity then simulating the emergence phase of this complex system. First, our findings reveal that the local scale is relevant to start a bottom-up planning approach on policy implementation. Second, the global challenges could be addressed on a regional scale if we investigate the local complexity to unfold the innovation flow over its complex ecosystem and lead the knowledge as a critical element for inclusive transition, most probably into cities. Finally, the innovation network is an existing fact which can translate as a host for prosperity; In this line of reasoning, we intend to spatialize the track of the innovation flow to achieve transition hotspots and respond adequately to upcoming world concerns.