Most discussions of Yamaga Soko's philosophical development as a Confucian scholar in Tokugawa Japan suggest that in his later years he moved away from Confucianism and toward a religio-philosophical celebration of Japan's supposed uniqueness. It is shown here, however, that Soko's nativism, set forth in his Chuchojijitsu, was later eclipsed by his final philosophical work, the Gengen hakki, wherein he articulated a kind of naturalistic numerology, based vaguely on the Yijing. This shift in Soko's thought can be viewed as a return to Neo-Confucianism, the earliest philosophical paradigm that he had embraced. Moreover, the successive shifts in his thinking can be understood in terms of the vicissitudes of his life, first in his exile to the Kansai area, near the ancient imperial capital of Kyoto, and then later in his pardon and return to Edo, the shogun's capital. Perhaps most importantly, this final shift in Soko's thought reveals that this prominent early modern thinker did reach his philosophical climax not in defiant opposition to Neo-Confucianism, nor in a sustained celebration of Japan's political traditions and their superlative nature, but instead in a return to modes of metaphysics akin to those typically deployed by Neo- Confucians themselves in their attempts to understand the changing nature of the cosmos and their political place within its flux.