God Almighty at that time revealed to him the calamities which threatened Malacca; both the pestilence and the war, with which it was to be afflicted in the years ensuing; and the utter desolation, to which it should one day be reduced for the punishment of its crimes.  For the inhabitants, who, since the arrival of the Father, had reformed their mariners, relapsed insensibly into their vices, and became more dissolute than ever, as it commonly happens to men of a debauched life, who constrain themselves for a time, and whom the force of ill habits draws backward into sin.  Xavier failed not to denounce the judgments of God to them, and to exhort them to piety, for their own interest.  But his threatenings and exhortations were of no effect:  and this it was that made him say of Malacca the quite contrary of what he had said concerning Meliapor, that he had not seen, in all the Indies, a more wicked town.

He embarked for Amboyna the 1st of January, 1546, with John Deyro, in a ship which was bound for the Isle of Banda.  The captain of the vessel was a Portuguese; the rest, as well mariners as soldiers, were Indians; all of them almost of several countries, and the greatest part Mahometans, or Gentiles.  The saint converted them to Jesus Christ during the voyage; and what convinced the infidels of the truth of Christianity, was, that when Father Xavier expounded to them the mysteries of Christianity in one tongue, they understood him severally, each in his own language, as if he had spoken at once in many tongues.

They had been already six weeks at sea, without discovering Amboyna; the pilot was of opinion they had passed it, and was in pain concerning it, not knowing how to tack about, because they had a full fore-wind.  Xavier perceiving the trouble of the pilot, “Do not vex yourself,” said he, “we are yet in the Gulph; and to-morrow, at break of day, we shall be in view of Amboyna.”  In effect, at the time mentioned, the next morning, they saw that island.  The pilot being unwilling to cast anchor, Father Xavier, with some of the passengers, were put into a skiff, and the ship pursued its course.  When the skiff was almost ready to land, two light vessels of pirates, which usually cruised on that coast, appeared on the sudden, and pursued them swiftly.  Not hoping any succour from the ship, which was already at a great distance from them, and being also without defence, they were forced to put off from shore, and ply their oars towards the main sea, insomuch that the pirates soon lost sight of them.  After they had escaped the danger, they durst not make to land again, for fear the two vessels should lie in wait to intercept them at their return.  But the Father assured the mariners, they had no further cause of fear:  turning therefore towards the island, they landed there in safety, on the 16th of February.