Japanese Christians were in a weaker position at the end of the 16th century than most realized, even though 250 churches had been established in the nation between 1549 and 1582.
From multiple sources, Japanese authorities were receiving alarming signals about what the long-term intentions of the visitors might be.

Some loud-mouthed Europeans were heard boasting that soon Japan would be a colony quite as subject to the Spanish empire as the Philippines was already.

Such stories were reinforced by several groups deeply hostile to the Jesuit missions – rival Catholic orders, notably the Dominicans, and Protestant travelers, English and Dutch.

Other more subtle signals pointed to the foreign nature of the faith, however hard the Jesuits tried to promote native clergy and a Japanese liturgy.

Warnings about foreign subversion found a ready audience in a new regime pledged to restore imperial unity.

By 1590, Japan was reunited by one of Nobunaga’s generals, Toyotomi Hideyoshi. By 1614, another warlord, Tokugawa Hidetada, was ruling the strongly centralized Shogunate regime that remained in power until 1868.

The new rulers had no sympathy for any movement that threatened to fracture Japanese unity, especially if that meant drawing in foreign imperialism. From the 1590s, Christians faced increasingly severe penal laws.

Once secular protectors were removed or deterred, the next obvious targets were the clergy themselves.

In 1597, Hideyoshi ordered the execution of 26 Christians, who were mutilated and then paraded for public display, before being publicly crucified in Nagasaki.

Local lords and daimyo were the first to withdraw their support, leaving the clergy and ordinary believers to face the consequences.

We know the names of at least 1,200 who perished between 1614 and 1630, and one day in 1622, 52 Christians were executed in Nagasaki by beheading and burning. This was “the Grand Martyrdom.”

One English visitor “saw 55 martyred at Miyako at one time … and among them little children 5 or 6 years old burned in their mother’s arms, crying out: ‘Jesus receive our souls.’ Many more are in prison who look hourly when they shall die, for very few turn pagans.”

Executions were accompanied by extraordinary tortures and mutilations, which were so extreme that even later Catholic martyrologists shied from describing them in detail.

Yet the recorded cases are only a tiny minority of the actual persecutions.

The martyrologies are heavily weighted toward remembering the names of Europeans and clergy, rather than of ordinary lay people or peasants, especially when these occurred in out-of-the-way corners of the land.

The complete roster of victims ran into many thousands, not counting those who were imprisoned, mutilated or had their property confiscated.

Under lethal pressure, by the 1630s Christians were able to survive only in a few areas where they retained the sympathy of local lords.

Even these refuges came under threat when Christians led the peasant rebellion in Shimabara in western Kyushu from 1637-38.

This uprising was only suppressed after battles in which the government mobilized 100,000 men, and tens of thousands of Christians were among those massacred in the war and the ensuing repression.

The outbreak was all the more terrifying to a society only just becoming accustomed to public order after long civil wars.

Worse, the crisis pointed yet again to the strength of Christians along the southern coasts, regions that could easily be the targets of future naval assault: Christian enclaves could become a fifth column for foreign empires.

The government decided that Christianity was a menace to national security that had to be utterly rooted out, and the draconian penal laws were fully enforced.

Already, in 1636, Japan had opted to become a wholly closed society, fearing that any European visitors might bring unwelcome Christian influences, or might even be clergy in disguise.

The government permitted very limited trade only with the Dutch, and then under rigidly limited circumstances.

In 1640, a party of foolhardy Portuguese visitors was refused entry with the warning that “While the sun warms the earth, let no Christian be so bold as to enter into Japan.”

Except for occasional martyrdoms recorded through the 18th century, Japanese Christianity largely vanished from official view.

The Japanese experience tells us much about the potential of religious persecution.

On occasion, persecution can and does succeed when applied with sufficient determination and violence, and repressive regimes did not need the technology available to a modern state, with its rich resources in means of communication and transportation.

Much of the Christian religious decline in the Middle East involves gradual, long-term force applied over centuries – massive pressures to conform, reinforced in extreme cases by ethnic cleansing.

In contrast, the Japanese story testifies to the power of governmental terror unleashed against a domestic population in intense bursts.

Contrary to the noble sentiment that is sometimes heard, you really can kill an idea.

Philip Jenkins is distinguished professor of history at Baylor University in Waco, Texas, and serves as co-director for the program on historical studies of religion in the Institute for Studies of Religion (ISR). He is the author of numerous books, including “Laying Down the Sword: Why We Can’t Ignore the Bible’s Violent Verses” (2011). A version of this article first appeared on The Anxious Bench, where he blogs regularly, and is used with permission.

Editor’s note: This is the second article of a two-part series. Part one is available here.

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