A priest, Juan Cobo, and an infantry captain were thereupon accredited to the Japanese Court as Philippine Ambassadors. On their arrival they were, without delay, admitted in audience by the Emperor; the treaty of commerce was adjusted to the satisfaction of both parties; and the Ambassadors, with some Japanese nobles, set sail for Manila in Japanese ships, which foundered on the voyage, and all perished.

Neither the political nor the clerical party in Manila was, however, dismayed by this first disaster, and the prospect of penetrating Japan was followed up by a second expedition.

Between the friars an animated discussion arose when the Jesuits protested against members of any other Order being sent to Japan. Saint Francis Xavier had, years before, obtained a Papal Bull from Pope Gregory XIII., awarding Japan to his Order, which had been the first to establish missions in Nagasaki. Jesuits were still there in numbers, and the necessity of sending members of rival religious bodies is not made clear in the historical records. The jealous feud between those holy men was referred to the Governor, who naturally decided against the Jesuits, in support of the Kingʼs policy of grasping territory under the cloak of piety. A certain Fray Pedro Bautista was chosen as Ambassador, and in his suite were three other priests. These embarked in a Spanish frigate, whilst Farranda Kiemon, who had remained in Manila the honoured guest of the Government, took his leave, and went on board his own vessel. The authorities bade farewell to the two embassies with ostentatious ceremonies, and amidst public rejoicings the two ships started on their journey on May 26, 1593. After 30 daysʼ navigation one ship arrived safely at Nagasaki, and the other at a port 35 miles further along the coast.

Pedro Bautista, introduced by Ferranda Kiemon, was presented to the Emperor Taycosama, who welcomed him as an Ambassador authorized to negotiate a treaty of commerce, and conclude an offensive and defensive alliance for mutual protection. The Protocol was agreed to and signed by both parties, and the relations between the Emperor and Pedro Bautista became more and more cordial. The latter solicited, and obtained, permission to reside indefinitely in the country and send the treaty on by messenger to the Governor of the Philippines; hence the ships in which the envoys had arrived remained about ten months in port. A concession was also granted to build a church at Meaco, near Osaka, and it was opened in 1594, when Mass was publicly celebrated.

In Nagasaki the Jesuits were allowed to reside unmolested and practise their religious rites amongst the Portuguese population of traders and others who might have voluntarily embraced Christianity. Bautista went there to consult with the chief of the Jesuit Mission, who energetically opposed what he held to be an encroachment upon the monopoly rights of his Order, conceded by Pope Gregory XIII. and confirmed by royal decrees. Bautista, however, showed a permission which he had received from the Jesuit General, by virtue of which he was suffered to continue his course pending that dignitaryʼs arrival.

The Portuguese merchants in Nagasaki were not slow to comprehend that Bautistaʼs coming with priests at his command was but a prelude to Spanish territorial conquest, which would naturally retard their hoped-for emancipation from the Spanish yoke.[2] Therefore, in their own interests, they forewarned the Governor of Nagasaki, who prohibited Bautista from continuing his propaganda against the established religion of the country in contravention of the Emperorʼs commands; but as Bautista took no heed of this injunction, he was expelled from Nagasaki for contumacy.

It was now manifest to the Emperor that he had been basely deceived, and that under the pretext of concluding a commercial and political treaty, Bautista and his party had, in effect, introduced themselves into his realm with the clandestine object of seducing his subjects from their allegiance, of undermining their consciences, perverting them from the religion of their forefathers, and that all this would bring about the dismemberment of his Empire and the overthrow of his dynasty. Not only had Taycosama abstained from persecuting foreigners for the exercise of their religious rites, but he freely licensed the Jesuits to continue their mission in Nagasaki and wherever Catholics happened to congregate. He had permitted the construction of their temples, but he could not tolerate a deliberate propaganda which foreshadowed his own ruin.[3]

Pedro Bautistaʼs designs being prematurely obstructed, he took his passage back to Manila from Nagasaki in a Japanese vessel, leaving behind him his interpreter, Fray Jerome, with the other Franciscan monks. An Imperial Decree was then issued to prohibit foreign priests from interfering with the religion of Japanese subjects; but this law having been set at naught by Bautistaʼs colleagues, one was arrested and imprisoned, and warrants were issued against the others; meanwhile the Jesuits in Nagasaki were in no way restrained.

The Governor of Nagasaki caused the Franciscan propagandists to be conducted on board a Portuguese ship and handed over to the charge of the captain, under severe penalties if he aided or allowed their escape, but they were free to go wherever they chose outside the Japanese Empire. The captain, however, permitted one to return ashore, and for some time he wandered about the country in disguise.

Pedro Bautista had reached Manila, where the ecclesiastical dignitaries prevailed upon the Governor to sanction another expedition to Japan, and Bautista arrived in that country a second time with a number of Franciscan friars. The Emperor now lost all patience, and determined not only to repress these venturesome foreigners, but to stamp out the last vestige of their revolutionary machinations. Therefore, by Imperial Decree, the arrest was ordered of all the Franciscan friars, and all natives who persisted in their adhesion to these missionariesʼ teachings. Twenty-six of those taken were tried and condemned to ignominious exhibition and death—the Spaniards, because they had come into the country and had received royal favours under false pretences, representing themselves as political ambassadors and suite—the Japanese, because they had forsworn the religion of their ancestors and bid fair to become a constant danger and source of discord in the realm. Amongst these Spaniards was Pedro Bautista. After their ears and noses had been cut off, they were promenaded from town to town in a cart, finally entering Nagasaki on horseback, each bearing the sentence of death on a breast-board.