Xavier, seeing the time of his departure drawing near, composed, in the Malaya tongue, a large instruction, touching the belief and morals of Christianity. He gave the people of Ternate this instruction written in his own hand, that it might supply his place during his absence. Many copies were taken of it, which were spread about the neighbouring islands, and even through the countries of the East. It was read on holidays in the public assemblies; and the faithful listened to it, as coming from the mouth of the holy apostle.
Besides this, he chose out some virtuous young men for his companions in his voyage to Goa, with design to breed them in the college of the company, and from thence send them back to the Moluccas, there to preach the gospel. These things being thus ordered, and the caracore, winch was to carry him to Amboyna, in readiness, it was in his thoughts to depart by night, in the most secret manner that he could, not to sadden the inhabitants, who could not hear of his going from them without a sensible affliction. But whatsoever precautions he took, he could not steal away without their knowledge. They followed him in crowds to the shore; men, women, and children, gathering about him, lamenting his loss, begging his blessing, and beseeching him, with tears in their eyes, "That since he was resolved on going, he would make a quick return."
The holy man was not able to bear these tender farewells without melting into tears himself. His bowels yearned within him for his dear flock; and seeing what affection those people bore him, he was concerned lest his absence might prejudice their spiritual welfare. Yet reassuring himself, by considering the providence of God, which had disposed of him another way, he enjoined them to meet in public every day, at a certain church, to make repetition of the Christian doctrine, and to excite each other to the practice of virtue. He charged the new converts to learn by heart the exposition of the apostles' creed, which he had left with them in writing; but that which gave him the greatest comfort was, that a priest, who was there present, promised him to bestow two hours every day in instructing the people, and once a-week to perform the same to the wives of the Portuguese, in expounding to them the articles of faith, and informing them concerning the use of the sacraments.
After these last words, Father Xavier left his well-beloved children in Jesus, and immediately the ship went off. At that instant an universal cry was raised on the shore; and that last adieu went even to the heart of Father Xavier.
Being arrived at Amboyna, he there found four Portuguese vessels, wherein were only mariners and soldiers, that is to say, a sort of people ill instructed in the duties of Christianity, and little accustomed to put them in practice, in the continual hurry of their life. That they might profit by that leisure which they then enjoyed, he set up a small chapel on the sea-side, where he conversed with them, sometimes single, sometimes in common, concerning their eternal welfare. The discourses of the saint brought over the most debauched amongst them; and one soldier, who had been a libertine all his life, died with such evident signs of true contrition, that being expired, Father Xavier was heard to say, "God be praised, who has brought me hither for the salvation of that soul;" which caused people to believe, that God Almighty had made a revelation of it to him.
By the same supernal illumination, he saw in spirit one whom he had left in Ternate in the vigour of health, now expiring in that place; for preaching one day, he broke off his discourse suddenly, and said to his auditors, "Recommend to God, James Giles, who is now in the agony of death;" the news of his death came not long after, which entirely verified the words of Xavier.
The four ships continued at Amboyna but twenty days, after which they set sail towards Malacca. The merchant-ship, which was the best equipped and strongest of them, invited the saint to embark in her; but he refused, out of the horror which he had for those enormous crimes which had been committed in her. And turning to Gonsalvo Fernandez, "This ship," said he, "will be in great danger; God deliver you out of it." Both the prediction and the wish of the saint were accomplished; for the ship, at the passage of the Strait of Saban, struck against a hidden rock, where the iron-work of the stern was broken, and little wanted but that the vessel had been also split; but she escaped that danger, and the rest of the voyage was happily performed.
The Father staying some few days longer on the isle, visited the seven Christian villages which were there; caused crosses to be set up in all of them, for the consolation of the faithful; and one of these crosses, in process of time, became famous for a great miracle, of which the whole country was witness.
There was an extreme drought, and a general dearth was apprehended. Certain women, who before their baptism were accustomed to use charms for rain, being assembled round about an idol, adored the devil, and performed all the magic ceremonies; but their enchantments were of no effect. A devout Christian woman knowing what they were about, ran thither, and having sharply reprehended those impious creatures, "As if," said she, "having a cross so near us, we had no expectations of succour from it; and that the holy Father had not promised us, that whatsoever we prayed for at the foot of that cross, should infallibly be granted." Upon this, she led those other women towards a river-side, where Xavier had set up a cross with his own hands, and falling down with them before that sacred sign of our salvation, she prayed our Saviour to give them water, to the shame and confusion of the idol. At the same moment the clouds began to gather on every side, and the rain poured down in great abundance. Then, all in company, they ran to the pagod, pulled it down, and trampled it under their feet; after which they cast it into the river, with these expressions of contempt, "That though they could not obtain from him one drop of water, they would give him enough in a whole river."
A faith thus lively, answered the hopes which the saint had conceived of the faithful of Amboyna. He compared them sometimes to the primitive Christians; and believed their constancy was of proof against the cruelty of tyrants. Neither was he deceived in the judgment he made of them; and they shewed themselves, when the Javeses, provoked by their renouncing the law of Mahomet, came to invade their island. While the Saracen army destroyed the country, six hundred Christians retired into a castle, where they were presently besieged. Though they were to fear all things from the fury of the barbarians, yet what they only apprehended was, that those enemies of Jesus Christ might exercise their malice against a cross which was raised in the midst of all the castle, and which Father Xavier had set up with his own hands. To preserve it, therefore, inviolable from their attempts, they wrapt it up in cloth of gold, and buried it in the bottom of the ditch. After they had thus secured their treasure, they opened the gate to the unbelievers, who, knowing what had been done by them, ran immediately in search of the cross, to revenge upon it the contempt which had been shown to Mahomet. But not being able to find it, they turned all their fury upon those who had concealed it, and who would not discover where it was.