Religion was a particularly thorny issue that Ieyasu’s two military predecessors, Nobunaga and Hideyoshi, had already begun to address. Collectively the policies of the three successive generalissimos led to the following situation. First, the upstart religion from the West, Christianity, was banned. The small numbers of Christians who refused to renounce their faith had to go underground. The squelching of the Christian movement in Japan was the precursor of closing Japan off from almost all contact with the outside world. This policy was initiated in 1639 and officially continued through 1854. Second, the Tendai Buddhist main temple on Kyoto’s Mount Hiei had grown to be the most powerful religious institution in Japan. In 1571 Nobunaga burned down the complex, destroying its three thousand buildings and its army of ten thousand warrior monks. Third, the most populist Buddhist religion of the time, the Shin Buddhist Honganji sect, had assembled a huge peasant army of its own that Nobunaga defeated in 1580. The sect then underwent a schism in 1603, breaking into Eastern and Western Honganji, thereby dividing the unity of this Buddhist group. And fourth, under Ieyasu the shogunate began to monitor the philosophical-religious schools of scholars, hoping to maintain at least some control over new developments and ideologies. Accompanying these four political events were intellectual circumstances equally important to the future of Shinto.
The key factors of intellectual change came to a head in the late sixteenth century when something philosophically new took hold in Japan. Throughout Japanese history there had been periods when Japanese groups (mainly religious or diplomatic) made the dangerous journey across the stormy Sea of Japan to the mainland, bringing back home cultural innovations and artifacts. In the fifteenth and sixteenth centuries especially, groups of Japanese Buddhist monks, mainly from the Zen tradition, went to the mainland to study. When they returned, they brought with them not only further materials related to Buddhism but also books from other philosophical traditions popular in China at the time. For our present concerns, the most significant items in their cargo were works of Chinese Neo-Confucianism. Although Zen Buddhist monastic scholars were studying the texts and introducing them to Japan, the books contained a philosophical system that would ultimately undermine the intellectual hegemony of Buddhism in the country. Neo-Confucianism was a sophisticated syncretistic philosophical movement in China that enriched traditional Confucian teachings with ideas from Buddhism and Daoism. By incorporating key ideas from these traditions into its own, Neo-Confucianism had disarmed the most powerful Buddhist and Daoist criticisms against Confucianism. As a result, from about the twelfth century up to the early twentieth century, Neo-Confucian philosophy (in various forms) generally dominated the Chinese intellectual scene.
These Neo-Confucian arguments against Buddhism entered Japan just before Tokugawa stability and peace brought rapid urbanization. The growth of city life supported schools of learning outside the traditional Buddhist temple complexes that had trained monk-scholars. The samurai (who needed job retraining to find a useful place in the peacetime society of the Tokugawa bureaucracy) and the aspiring merchant class (who needed to acquire culture fast) frequented such urban schools. Furthermore, the increasingly literate urbanites created a demand for widely distributed, printed publications. By the late seventeenth century, literary culture, including philosophy, was thriving in the cities.