Other missionaries arriving in 1560, the circle of operations was extended; but shortly afterward the revolution, headed by Mori, compelled Vilela to leave Kioto, where he had settled, and a simultaneous outbreak in Omura necessitated the withdrawal of the missionaries stationed there. Mori, of Choshiu, was perhaps the most powerful noble of the day, possessing no fewer than ten provinces, and, as he was throughout an open enemy to Christianity, his influence was exercised against it with much ill result.
On Vilela's return to Kioto from Sakai, where a branch mission had been established, he succeeded in gaining several distinguished converts. Among these were Takayama, a leading general of the time, and his nephew. He did not, however, remain long in the capital. The recurrence of troubles in 1568 made it necessary for him to withdraw, and he then proceeded to Nagasaki, where he met with considerable success. In this same year we come across Valegnani preaching in the Goto Isles, and Torres in the island of Seki, where he died. Almeida, too, about this time founded a Christian community at Shimabara, afterward notorious as the scene of the revolt and massacre of the Christians.
Hitherto we find little mention of Christianity in Japanese books. This may partly be explained by the fact that the labors of the missionaries were chiefly confined to the southern provinces, Christianity having as yet made little progress at Kioto, the seat of literature. But the scarcity of Japanese records can scarcely be wondered at in the face of the edict issued later in the next century, which interdicted not only books on the subject of Christianity, but any book in which even the name of Christian or the word Foreign should be mentioned.
Short notices occur in several native works of the arrival in Kioto at this date of the Jesuit missionary Organtin, and some curious details are furnished respecting the progress of Christianity in the capital and the attitude of Nobunaga in regard to it.
The Saikoku Kirishitan Bateren Jitsu Roku, or "True Record of Christian Padres in Kiushiu," gives a minute account of the appearance and dress of Organtin, and goes on to say: "He was asked his name and why he had come to Japan, and replied that he was the Padre Organtin and had come to spread his religion. He was told that he could not be allowed at once to preach his religion, but would be informed later on. Nobunaga accordingly took counsel with his retainers as to whether he should allow Christianity to be preached or not. One of these strongly advised him not to do so, on the ground that there were already enough religions in the country. But Nobunaga replied that Buddhism had been introduced from abroad and had done good in the country, and he therefore did not see why Christianity should not be granted a trial. Organtin was consequently allowed to erect a church and to send for others of his order, who, when they came, were found to be like him in appearance. Their plan of action was to tend the sick and relieve the poor, and so prepare the way for the reception of Christianity, and then to convert everyone and make the sixty-six provinces of Japan subject to Portugal."
The Ibuki Mogusa gives further details of this subject, and says that the Jesuits called their church Yierokuji, after the name of the period in which it was built, but that Nobunaga changed the name to Nambanji, or "Temple of the Southern Savages." The word Namban was the term usually applied to the Portuguese and Spaniards.
During the next ten years Organtin and other missionaries worked with considerable success in Kioto under Nobunaga's immediate protection. This period is also remarkable for the conversion of the Prince of Bungo, who made open profession of Christianity and retired into private life, and for the rapid progress which the new doctrine made among the subjects of Arima-no-Kami. This good fortune was again counterbalanced by the course of events in the Goto Islands, where Christianity lost much ground owing to a change of rulers.
Ten years thus passed away, when the Christian communities sustained great loss in the disgrace of Takayama, who was banished to Kaga for taking part in an unsuccessful intrigue against Nobunaga which was headed by the Prince of Choshiu. Takayama's nephew, Ukon, however, declared for Nobunaga, and the latter gave a further proof of his friendly feeling toward Christianity by establishing a church in Adzuchi-no-Shiro, the castle town which he had built for himself in his native province of Omi.
In 1582 a mission was sent to the papal see on the part of the Princes of Bungo and Omura, and Arima-no-Kami. This mission was accompanied by Valegnani, and reached Rome in 1585, returning five years later to Japan.
In the following year Nobunaga was assassinated and Hideyoshi, who succeeded him in the chief power, was content, for the first three or four years of his administration, to follow in the line of policy marked out by his predecessor. Christianity, therefore, progressed in spite of the drawbacks caused by the frequent feuds between the southern daimios, and seminaries were established under Hideyoshi's auspices at Osaka and Sakai. During this period Martinez arrived in the capacity of bishop; he was charged with costly presents from the Viceroy of Goa to Hideyoshi, and received a favorable audience.