History of the Catholic Church in Japan:
Francis Xavier and the Jesuits arrived in Japan in the 1540s and soon had over 100,000 converts and at first were welcomed by the Imperial governments, and Christianity took root. It became especially strong in the area around Nagasaki.
Unfortunately their good relationship with the Imperial government did not last. Fearful of colonialism that they had seen from the Spanish and Portuguese in the Philippines, the Emperor Ogimachi issued edicts to ban Catholicism in 1565 and again in 1568. Although these did not have the effect desired, in 1587 the Imperial Regent banned the Jesuit missionaries, and Christianity was repressed as a threat to national unity. Practicing Catholics were forced to go underground, becoming hidden Christians, and many were persecuted and killed. Many martyrs were produced over the next few centuries.
Catholic shrines & places of interest in Japan:
Akita: Shrine of Our Lady of Akita
Otometoge: Maria Seido Chapel (dedicated to the martyrs of Nagasaki)