Philip Jenkins here tells the largely untold story of the persecution and extermination of Christians in Japan. The whole article is worth your close reading.
A few points which Dr. Jenkins makes are that religious persecution is not limited to the likes of Christianity and Islam, but is also capable of existing within Buddhism and Shintoism, Christianity’s “European” character must be understood in terms of direct action on the part of other world cultures (ie. persecution) as much as anything else, and finally, and most disturbingly, sometimes religious persecution works. He believes that the absence of any meaningful Christianity in Japan can be traced back to these 17th century persecutions.