Some scholars say Japan’s Christian history began long before the so-called “Christian century” (1549-c.1640). Their claim takes us all the way back to 7th- and 8th-century Nara, where Nestorian Christians from Persia are said to have built churches, operated a leper hospital and even converted the Empress Komyo, wife of the devout Buddhist, Emperor Shomu (reigned 724-749), to Christianity.

The evidence is tantalizing but inconclusive. If they existed, Nara’s early Christians left no mark on the culture. Spanish and Portuguese Jesuit missionaries who arrived some 800 years later not only had to start from scratch, they had to define scratch. How to begin to explain, in an alien language, such alien and mysterious concepts as transcendent Godhead, the Virgin Birth, the sacrifice on the Cross of the Son of God for the redemption of mankind?

The scale of the task is a measure of the determination of the men who faced it, and Francis Xavier, the Basque Jesuit whose landing at Kagoshima in August 1549 inaugurates the “Christian century,” was nothing if not determined.

A prayer attributed to him begins, “Eternal God, Creator of all things, remember that the souls of unbelievers have been created by thee and formed to thy own image and likeness. Behold, O Lord, how to thy dishonor hell is being filled with these very souls . . . Do not permit, O Lord, I beseech thee, that thy divine Son be any longer despised by unbelievers . . .

Thus fortified, the future saint went to work on the Japanese.

Xavier had by then been in Asia seven years. He arrived in Goa, “the Rome of India,” capital of Portugal’s Far Eastern empire, in 1542. He traveled vast distances, much of his missionary work unfolding among cannibals and warriors of remote South Asian islands.

In 1547 he was on his way back to Goa when he heard at Malacca, in today’s Malaysia, encouraging reports of a new Asian discovery. Four years earlier some Portuguese traders blown off-course by a storm had been the first Europeans known to set foot in Japan. “There,” wrote Xavier, “according to the Portuguese, much fruit might be gained for the increase of our holy faith, more than in any other part of the Indies, for they are a people most desirous of knowledge, which the Indian heathen are not.”

At Malacca he met a Japanese, a sometime pirate named Yajiro: “He came to seek me with a great desire to know about our religion.” Yajiro, christened Paul, became Xavier’s companion and interpreter. He proved a mixed blessing.

Japan in the 16th century was disintegrating. Feudal lord fought feudal lord; combat had become endemic. “There was not a province in Japan,” writes the historian George Sansom, “free from the armed rivalry of territorial barons or lords of the [Buddhist] church.” Few in 1549 would have foreseen the firmly united nation that was to emerge 50 years later.

Nor was there much in Xavier’s first faltering steps in this unknown land to suggest the groundswell of success soon to reward the Jesuits’ unshakable confidence and dedication. The success was brilliant but fleeting. It ended tragically in what Engelbert Kaempfer, a German physician and chronicler stationed at Nagasaki early in the 18th century, called “the most cruel persecution and torture of Christians ever witnessed on this globe . . . lasting more than 40 years until the last drop of Christian blood was spilled.”

“For non-Christians,” writes theologian Stephen Turnbull in “The Kakure Kirishitan of Japan” (see accompanying story), “stamping on the fumie eventually acquired the air of an annual ritual eagerly awaited as one of the many New Year celebrations, but to the [Christians], fumie never lost its horror, even in cases where the authorities required only the outward sign of apostasy . . . Prayers were said to counteract the blasphemy, and in one community there was a ritual of burning the straw sandals worn when treading on the image, mixing the ashes with water and drinking the result.”

The pit was said to be the most horrible torture of all. Historian C.R. Boxer describes it: “The victim was tightly bound around the body as high as the breast (one hand being left free to give the signal of recantation) and then hung downwards from a gallows into a pit which usually contained excreta and other filth, the top of the pit being level with his knees. In order to give the blood some vent, the forehead was lightly slashed with a knife. Some of the stronger martyrs lived for more than a week in this position, but the majority did not survive more than a day or two.”

The “Christian Century” ends with the Shimabara rebellion of 1637-38. Ivan Morris calls it a “holocaust,” a word no modern historian would use lightly. The Shimabara Peninsula in western Kyushu was then a desperately poor outback whose starved peasants were mercilessly squeezed for taxes far beyond their capacity to pay. Default invited torture as ghastly and imaginative as that meted out to Christians. How much the uprising was motivated by poverty and how much by Christian ideals remains in dispute. Its leader was a charismatic 15-year-old named Amakusa Shiro, known to his followers as “heaven’s messenger.” Miraculous powers were attributed to him.

Ensconsed in the abandoned Hara Castle that they seized as their stronghold were 37,000 rebels — peasants and low-ranking samurai, all at least nominally Christian. For five months they held out against impossible odds, but the end, barring a miracle, was never in doubt.

“The slaughter on 15th April [1638],” writes Morris, “was one of the greatest in all Japan’s sanguinary history. The nearby rivers and inlets were clogged with decapitated bodies.”

Amakusa Shiro was beheaded, his head publicly gibbeted in Nagasaki. Rebels who weren’t massacred hurled themselves into the flames of the burning castle. Morris quotes a contemporary daimyo — steeped in samurai rather than Christian ideals — as commenting, “For people of their low station this was indeed a praiseworthy way of dying. Words cannot express [my admiration].”

Shimabara marks Japan’s retreat into more than 200 years of isolation from the outside world. It also marks the end, until modern times, of open Christian worship in Japan. For the next two centuries the story of Japanese Christianity is that of the “Kakure Kirishitan,” the “Hidden Christians.”

Michael Hoffman’s latest book, “Birnbaum: A Novel of Inner Space,” will be published early next year by Printed Matter Press. His Web site can be found at www.michaelhoffman.squarespace.com

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