Although there is some speculation that Christianity first arrived in Japan with Nestorian missionaries, the genesis of Christianity in Japan came with Francis Xavier, a Catholic Jesuit missionary who first brought the faith to many different parts of Asia.
At this time, Europeans viewed many of the peoples of Asia as uncivilized and barbaric; Japan, however, was different. Xavier immediately recognized that the Japanese were civilized and even sophisticated, and quite different from what he had encountered in India. Landing in Kagoshima - the southernmost prefecture of Japan's main island, Honshu - Xavier hoped to convert the people of Japan, but first and foremost he wanted to meet the Emperor, bringing presents in an attempt to secure an audience.
The early evangelization of Japan isn't just an isolated historical situation, but can teach us much about the present church - and gives us an opportunity to learn and understand where the Jesuit missions in Japan went wrong. A major part of this was the intertwining of church and state. The governments of exploration-minded European powers like Spain and Portugal - which provided the bulk of early missionaries to Japan - weren't just interested in evangelizing; they intended to secure power and trade in Asia, and missions were closely tied to this.
Only decades later, Christianity was outlawed, and believers were violently persecuted. While this may have been an inevitable outcome, I don't believe that's true. The problem was with the conceptual approach to missions; the early Jesuit missionaries went for a top-down style of missions, converting the powerful and influential, which would then trickle down to the common people. This isn't without precedent in the Apostolic period - we have accounts in scripture of Paul and other missionaries converting an influential individual, whose family soon follows. The problem is that this approach immediately singled out Christianity as a subversive force, probably serving European interests that sought to undermine Japanese and seize power during the tumultuous Warring States period.
For a time, though, the Catholic strategy worked, and Christianity expanded and was received favorable in parts of Western Japan. Nagasaki was not just a fruitful area for missions, it was virtually self-sufficient. The Jesuit missions were eventually financed by the economic endeavors of missions in Asia, not primarily by Europeans or by the laity.
Almost from its inception, the Japanese church was heavily intertwined with politics and economics. While this helped the church to "get ahead" and gain support from some Japanese rulers who wanted access to European wares such as ingredients for making gunpowder, it came at a cost. The intermingling of Christianity and politics was ultimately responsible for the sudden change of fortunes in the church. Only decades after its introduction, and tens of thousands of converts later, Christianity was made illegal, and violently persecuted.
To some extent, the Church will always intersect with the economic and political worlds, but the Japanese case clearly shows the dangers of this approach. It didn't just cost the Jesuits their mission in Japan - it resulted in one of the worst persecutions in history, which almost entirely succeeded in wiping out Christianity in Japan for hundreds of years. Christianity moved underground as the Hidden Christian movement, where the faith was handed down in secret, fragmented form until the late 19th century, when Protestant missionaries entered the country for the first time.
I can't help but wonder, what if things had been different? What if the missionaries to Japan had been less worried about self-sufficiency and working for the interest of their home countries, rather than God's Kingdom? If the missionary efforts had focused squarely on the common people and avoided choosing sides in politics, then perhaps the Christian church would not have been seen as a political threat, and such vehement persecution could have been avoided.
The early Japanese church shows the risk of faith becoming intertwined in political interests. While many American Christians lament the declining influence of Christianity in civic life, the basic problem is that when our faith becomes the dominant political force, the Law drowns out the Gospel. Japan's early experience with Christianity could have been quite different if this had been better understood. But while it's too late to change Japan's past, it's not too late to learn from it as we consider the relationship of church and state today.