This chapter adopts a data-driven regional science approach and proposes a “post-third stage” in the evolution of Japan’s regional economic structure, building on the seminal three-stage model of Fujita and Tabuchi (Regional Science and Urban Economics 27(6): 643–670, 1997). It argues that the monocentric concentration around Tokyo, once dominant, has gradually shifted toward interregional convergence since the 2000s, although Tokyo continues to play a leading role. This shift is not driven solely by physical dispersion but is increasingly supported by network-based scale externalities, conceptualized as Borrowed Size, as well as institutional thickness and relational proximity at the prefectural level. The chapter provides both empirical evidence and theoretical elaboration on this transformation, suggesting a redefinition of spatial dynamics in which functional connectivity and institutional collaboration outweigh physical agglomeration. This perspective carries significant implications for both regional development theory and spatial policy design.