Jesuit missionaries arrived in Japan in the sixteenth century and the result was extraordinary. Missions thrived and the Jesuits themselves became extremely important as a liaison between Japan and the West. Christians established churches, printing presses, hospitals, universities, so that as the seventeenth century rolled around, the Catholic community in Japan was the largest Catholic community in the world that was not under the direct governance of some European power. In the 1610s, Nagasaki, the "Rome of Japan", had ten Catholic churches and was mostly Catholic. One wonders what would have happened if things had gone a different way.
The way things actually went was into shadow and darkness. Toyotomi Hideyoshi unified Japan, and began to be worried that the Catholics represented a way for European powers to manipulate Japanese policy. In 1587 he issued a ban on Catholicism. It really wasn't enforced, and famously Hideyoshi himself still chatted with Jesuits in his gardens. But it was a shift. Technically, all Catholics were in violation of the law, and technically they only continued under the suffrage of the powers of Japan. When collapses like this come, they do not come all at once but in little ripples, followed by little waves, followed by greater waves, followed by terrible ones. And every so often, those powers would move under the law to remind everyone of the state of things. In 1597, St. Paul Miki and his twenty-five companions were crucified in Nagasaki. When Tokugawa Ieyasu took over after Hideyoshi, English and Dutch traders, seeing an opening, did not waste time filling his ears with the dangers of Jesuits. Under the next Tokugawa shogun, Hidetada, a persecution broke out in 1613, and in 1614 all missionaries were expelled from Japan. And in the next shogunate, that of Iemitsu, in 1632, another persecution broke out and Catholicism was banned entirely. A rebellion, the Shimabara Rebellion, broke out; the Rebellion was not purely religious in nature, but a lot of the participants were Catholic peasants. It was squashed ruthlessly. The persecution was continual and vigorous from that point, and the Tokugawa shoguns destroyed every visible sign of Catholicism. Christianity in Japan fell into shadow and darkness. And silence.
But it did not die. In quiet, Japanese Catholics continued. They had no priests, and so only had baptisms and marriage as their sacraments, but they baptized their children and taught them basic catechism and fragments of old prayers. They would enroll as Buddhists and build little shrines ostensibly to Guanyin, Kannon in Japanese, bodhisattva of compassion, who had sometimes been represented with a child on her knee; really it was the Virgin Mary, and often there would be some cross, surreptitious and easy to miss, to mark the difference. Little pieces, sometimes garbled, sometimes disarrayed, fragments, some strands of the broken web did not break. And in the Meiji Restoration decades later, when the Paris Foreign Missions Society built Oura Church in Nagasaki, they found, to their surprise, a steady stream of people from all around Nagasaki, wanting to see what a statue of the Virgin Mary looked like that wasn't hidden as a Maria Kannon, or wanting to talk to a real priest from Rome about how to catechize their children. Chopped away at bough and stalk until there seemed to be nothing left, the tree had not been uprooted.
The fortnightly book is the most famous novel about the Catholic persecution in Japan, and is often considered one of the great novels of the twentieth century, by Shusaku Endo. The title is Chinmuku, or Silence. I've had it on my shelves for quite some time, but never actually finished it, for reasons having nothing to do with the novel itself. It is a historical novel depicting events around the time of the Shimabara Rebellion, as the persecution became ruthless and total. While the main character is fictional, the book opens with an event that was not: the apostasy of Cristóvão Ferreira. Ferreira was the Jesuit superior for the mission. He was captured and tortured in the pit, and he broke and became a collaborator. It was a shock both in and out of Japan.
The translation I'll be using is the standard English one, by William Johnston.