Martyrdoms
In 1596 the Spanish ship San Felipe foundered off Shikoku and the Japanese confiscated it's rich cargo. A controversy among Japanese, Jesuits and Friars resulted; Hideyoshi once more turned anti- Christian and condemned to death the Franciscans and their parishioners in Kyoto. Twenty six Christians both foreigners and Japanese were crucified at Nagasaki in 1597. No further hostile action was taken, and missionary work continued unobtrusively. By this time the church had reached it's greatest expansion, with the number of Christians being estimated at 300,000. Tokugawa Ieyasu, who became the defacto ruler in 1600, was at first willing to tolerate the missionaries' presence for the sake of profitable Portuguese trade, but the arrival of the protestant Dutch and English merchants. allowed him to act more freely against the Catholic missionaries. As the final showdown between Ieyasu and Toyotomi Hideyori, son of the late Hideyoshi, approached Ieyasu turned against the Church, knowing his rival commanded considerable support in western Japan, where the Christian influence was strongest. Ieyasu was victorious, and in 1614 the Tokugawa shogunate ordered missionaries to leave the country; most of them departed but some 40, including Japanese priests, remained to continue their work undercover.
Persecution and Suppression
Within a few year organized persecution commenced. In 1622, 51 Christians were executed at Nagasaki, and two years later 50 were burned alive in Edo(now Tokyo). A total of 3000 believers are estimated to have been martyred; this figure does not include the many who died as the result of sufferings in prison or in exile. In 1633 some 30 missionaries were executed, and by 1637, only five were left at liberty. The Shimabara uprising of 1637-38 prompted the government to sever contacts with the west, except for some merchants of the Dutch east India company, confined to Dejima. Subsequent missionary attempts to enter and work in the country were unsuccessful.
The Japanese are noted for there religious tolerance, and the persecution was occasioned by social and political rather than purely religious factors. Christian exclusivism, with its unwillingness to tolerate other religions, aroused resentment in some circles. Missionaries were regarded as a potential fifth column preparing the way for Iberian colonialism. More significantly, the shogunate was on the alert for any coalition of disaffected elements that might threaten its hegemony, and Christianity was viewed as a possible catalyst. Finally, Christian insistence on the primacy of the individual's conscience was regard as subversive in a society that attached overwhelmingly importance to unconditional obedience to superiors.
Reintroduction
Japan's period of isolation ended in the mid-19th century, when Westerners were again allowed to enter the country. In 1859 a Catholic priest took up an appointment as interpreter for the French consulate in Edo, and in the same year representatives of three Protestant churches reached Japan. Ostensibly these ministers came to serve foreign residents, but there true aim was to begin direct work among the Japanese.