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The nail in the coffin for missionary presence and activity in Japan was, arguably, a Christian [[Shimabara Rebellion|uprising at Shimabara]] in [[1637]]-[[1638]], in which tens of thousands of Christians rebelled against their lord; roughly 37,000 Christians were killed before the rebellion was over. The event was seen by the shogunate as evidence of the divided loyalties of Japanese Christians, and a spectre of rebellions, divisions, and instability which would continue if Christianity were not violently and powerfully suppressed.

The nail in the coffin for missionary presence and activity in Japan was, arguably, a Christian [[Shimabara Rebellion|uprising at Shimabara]] in [[1637]]-[[1638]], in which tens of thousands of Christians rebelled against their lord; roughly 37,000 Christians were killed before the rebellion was over. The event was seen by the shogunate as evidence of the divided loyalties of Japanese Christians, and a spectre of rebellions, divisions, and instability which would continue if Christianity were not violently and powerfully suppressed.

Missionaries were expelled finally and entirely in [[1639]], and Christianity banned. Representatives of the [[Dutch East India Company]], merchants with little interest in proselytizing, were now the only Europeans allowed direct intercourse with Japan, and as of [[1641]], they were restricted to the tiny manmade island of [[Dejima]] in Nagasaki. Many Japanese converts remained, however, as so-called "[[hidden Christians]]" (''kakure Kirishitan''), some finding success in hiding in remote areas, such as the island of [[Ojika]] off Nagasaki, where a ''kakure Kirishitan'' church still stands. At least one Jesuit is known to have snuck into Japan during this period of [[kaikin|maritime restrictions]]: [[Giovanni Battista Sidotti]] entered Japan in [[1708]], was interrogated by Confucian scholar & chief shogunal advisor [[Arai Hakuseki]], and was imprisoned, dying in his cell in [[1714]].

Missionaries were expelled finally and entirely in [[1639]], and Christianity banned. Representatives of the [[Dutch East India Company]], merchants with little interest in proselytizing, were now the only Europeans allowed direct intercourse with Japan, and as of [[1641]], they were restricted to the tiny manmade island of [[Dejima]] in Nagasaki. Mancio Konishi (b. 1600), a Japanese convert who was ordained in Rome and returned to Japan in 1632, may have been the last remaining Catholic priest in Japan when he was finally captured and killed by the authorities in 1644.<ref>de Bary, et al, ''Sources of Japanese Tradition'', 146n2.</ref> Many Japanese lay converts remained, however, as so-called "[[hidden Christians]]" (''kakure Kirishitan''), some finding success in hiding in remote areas, such as the island of [[Ojika]] off Nagasaki, where a ''kakure Kirishitan'' church still stands. At least one Jesuit is known to have snuck into Japan during this period of [[kaikin|maritime restrictions]]: [[Giovanni Battista Sidotti]] entered Japan in [[1708]], was interrogated by Confucian scholar & chief shogunal advisor [[Arai Hakuseki]], and was imprisoned, dying in his cell in [[1714]].

Once the ban on Christianity was lifted, in the [[Bakumatsu Period]], the Jesuit order re-entered Japan, and retains a degree of presence today; [[Sophia University]] in Tokyo, founded in 1913 at the request of the Pope as the first Jesuit university in Japan, is generally regarded as among the top three private universities in the city.

Once the ban on Christianity was lifted, in the [[Bakumatsu Period]], the Jesuit order re-entered Japan, and retains a degree of presence today; [[Sophia University]] in Tokyo, founded in 1913 at the request of the Pope as the first Jesuit university in Japan, is generally regarded as among the top three private universities in the city.