Francis Xavier was the first Jesuit priest to work in Japan. He arrived in 1549, six years after Portugal started trade relations with Japan. He was under the guidance of his interpreter Anjiro, who had fled Japan under charge of murder and told Francis about Japanese life and customs. Francis arrived in Japan as a representative of the Portuguese king, and was well received in Japan.
Francis struggled to translate certain concepts of Christianity into Japanese, both because of language and cultural barriers. These included a benevolent God who nevertheless created evil and the concept of God. He adapted some aspects of Christianity to Buddhism teachings, and ultimately spent two years in Japan as a missionary before returning to work in India.
Missionary activity in Japan reached its height in the 1570s -- a time at which there were over 100,000 Japanese converts. There were mainly centered in the Kyushu region, but their effect was felt nation-wide, with converts across the country in smaller numbers. The religion also did not favor rich or poor, with people of all social standings participating in Christian life.
In the 1580s, Hideyoshi unified Japan and wanted to reduce the threats of European powers in Japan. Hideyoshi banned Catholicism in 1587, and over the next several decades successive waves of persecution would break out, and Catholics would be executed. The method of apostasy involved pictures of the Virgin Mary and Christ, called fumie, which people were forced to trample on. If they would not renounce their faith they were sent to Nagasaki to be converted away, and if this did not work they would be executed on Mount Unzen.
Catholics who kept practicing their religion in secret were called "Kakure Kirishitan," or Underground Christians. Much of this community survived in secret until Japan was re-opened to foreign influence in 1853 by Matthew Perry. Some rejoined the Catholic Church and others continued to practice their own religion.