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Founded before 1500, Nagasaki was originally secluded by harbors. It enjoyed little historical significance until contact with European explorers in 1542, when a Portuguese ship accidentally landed nearby, somewhere in Kagoshima prefecture. The Jesuit missionary Francis Xavier arrived in another part of the territory in 1549, but left for China in 1551 and died soon afterwards. His followers who remained behind converted a number of daimyo (feudal lords). The most notable among them was Omura Sumitada, who derived great profit from his conversion through an accompanying deal to receive a portion of the trade from Portuguese ships at a port they established in Nagasaki in 1571 with his assistance.
The little harbor village quickly grew into a diverse port city, and Portuguese products imported through Nagasaki (such as tobacco, bread, tempura, textiles and a Portuguese sponge-cake called castellas) were assimilated into popular Japanese culture. The Portuguese also brought with them many goods from China.
Due to the instability during the Warring States period, Sumitada and Jesuit leader Alexandro Valignano conceived a plan to pass administrative control over to the Society of Jesus rather than see the Catholic city taken over by a non-Catholic daimyo who was quickly ascending to power in Kyūshū. Thus, for a brief period after 1580, the city of Nagasaki was a Jesuit colony, under their administrative and military control. In 1587, however, Toyotomi Hideyoshi's campaign to unify the country arrived in Kyūshū. Concerned with the large Christian influence in southern Japan, as well as the active and somewhat arrogant role the Jesuits were playing in the Japanese political arena, Hideyoshi ordered the expulsion of all missionaries, and placed the city under his direct control. However, the expulsion order went largely unenforced, and the fact remained that most of Nagasaki's population remained openly practicing Catholics.
In 1596, the Spanish ship San Felipe was wrecked off the coast of Shikoku, and Hideyoshi learned from its pilot (so says the Jesuit account) that the Spanish Franciscans were the vanguard of an Iberian invasion of Japan. In response, Hideyoshi ordered the deaths of 26 Catholics in Nagasaki on Feb. 5 of that year. Portuguese traders were not ostracized, however, and so the city continued to thrive.
In 1602, Augustinian missionaries also arrived in Japan, and when Tokugawa Ieyasu took power in 1603, Catholicism was still grudgingly tolerated. Many Catholic daimyo had been critical allies at the Battle of Sekigahara, and the Tokugawa position was not strong enough to move against them. Once Osaka Castle had been taken and Toyotomi Hideyoshi's offspring killed, though, the Tokugawa dominance was assured. In addition, the Dutch and English presence allowed trade without religious strings attached. Thus, the hammer fell in 1614, with Catholicism officially banned and all missionaries ordered to leave. Most Catholic daimyo apostatized, and forced their subjects to do so, although a few would not renounce the religion and left the country as well. A brutal campaign of persecution followed, with thousands across Kyūshū and other parts of Japan killed, tortured, or forced to renounce their religion.
Catholicism's last gasp as an open religion, and the last major military action in Japan until the Meiji Restoration, was the
Shimabara rebellion of 1637. While there is no evidence that Europeans directly incited the rebellion, Shimabara had been a Christian han for several decades, and the rebels adopted many Portuguese motifs and Christian icons. Consequently, in Tokugawa society the word "Shimabara" solidified the connection between Christianity and disloyalty, constantly used again and again in Tokugawa propaganda.
The Shimabara rebellion also convinced many policy-makers that foreign influences were more trouble than they were worth. The Portuguese, who had been previously living on a specially-constructed island-prison in Nagasaki harbor called Deshima, were expelled from the archipelago altogether, and the Dutch were moved from their base at Hirado into the trading island. In 1720 the ban on Dutch books was lifted, causing hundreds of scholars to flood into Nagasaki to study European science and art. Consequently, Nagasaki became a major center of rangaku, or "Dutch Learning". During the Edo period, the Tokugawa shogunate governed the city, appointing a hatamoto, the Nagasaki bugyō, as its chief administrator.
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