The viceroy of the Indies, upon the complaints which were brought against Don Alvarez for his tyrannical proceedings, deprived him of the government of Malacca; and causing him to be brought to Goa as a prisoner of state, sent him to Portugal under a sufficient guard. There all his goods were confiscated to the king's exchequer; and for himself, he was condemned to perpetual imprisonment Before his departure from the Indies, he had gotten an obscene disease, which increased to that degree in Europe, that he died of it at last in a shameful manner, no remedy availing to his cure; the stench of his polluted body having first made him insupportable to all the world. As for Pereyra, who had sacrificed his whole estate for the benefit of souls, and propagation of the faith, though the governor had so unjustly made a seizure of his fortunes, yet King John III. restored him all with interest, and heaped his royal favours on him in succeeding years, according to the prediction of the Father.
But the devotion of the people failed not of an Immediate reward. The pestilence, which for some weeks had laid waste the town, as the saint had foretold not long before his death, in his letter to Father Francis Perez, on the sudden ceased; insomuch, that no infection was from thenceforward caught; and they, who had been infected, were cured, without taking any remedy. Besides this contagious disease, the famine raged to that degree, that multitudes of people daily died of hunger. This second judgment was likewise diverted at the same time; for, together with the vessel, which bore the sacred body, there came in a fleet of ships, which were laden with all manner of provisions, to supply the necessities of the town.
These so considerable favours ought to have obliged the inhabitants to have honoured the body of their benefactor with a sepulchre which was worthy of him. In the mean time, whether the fear of their governor withheld them, or that God permitted it for the greater glory of his servant, having taken the body out of the chest, they buried it without the church, where the common sort of people were interred; and, which was yet more shameful, they made the grave too scanty; so that crushing the body to give it entrance, they broke it somewhere about the shoulders, and there gushed out blood, which diffused a most fragrant odour. And farther, to carry their civility and discretion to the highest point, they trampled so hard upon the earth, which covered the blessed corpse, that they bruised it in many parts; as if it had been the destiny of that holy man to be tormented by the people of Malacca, both during his life, and after his decease. The sacred corpse remained thus without honour, till the month of August, when Father John Beyra came from Goa, in his return to the Moluccas, with two companions whom Gaspar Barzæus, the vice-provincial, had given him, pursuant to the orders of Father Xavier. This man, having always had a tender affection for the saint, was most sensibly afflicted for his death; and could not think of continuing his voyage to the Moluccas, till he had looked upon the body, of which so many wonders were related. Opening himself on that subject to James Pereyra, and two or three other friends of the dead apostle, they took up his body privately one night. The corpse was found entire, fresh, and still exhaling a sweet odour; neither had the dampness of the ground, after five months burial, made the least alteration in him: they found even the linen which was over his face tinctured with vermilion blood.
This surprising sight so wrought upon their minds, that they thought it their duty, not to lay it again into the ground, but rather to contrive the means of transporting it to Goa. Pereyra ordered a coffin to be made of a precious wood, and after they had garnished it with rich China damask, they put the corpse into it, wrapping it in cloth of gold, with a pillow of brocard underneath the head. The coffin was afterwards bestowed in a proper place, known only to the devoted friends of Father Xavier; and it pleased the Almighty to declare, by a visible miracle, that their zeal was acceptable to him: For a waxen taper, which they had lighted up before the coffin, and which naturally must have burnt out within ten hours, lasted eighteen days entire, burning day and night; and it was observed, that the droppings of the wax weighed more than the taper itself at the beginning.
In the mean time an occasion offered for the voyage of the Moluccas, while they were waiting for an opportunity of passing to Goa. Beyra, therefore, put to sea, more inflamed than ever with the zeal of souls; and filled with a double portion of an apostolic spirit, which the sight of the saint had inspired into him. But of the two companions which had been assigned for the mission of the Moluccas, he left one behind him at Malacca, to be a guardian of that holy treasure, and this was Emanuel Pavora. Peter de Alcaceva at the same time returned from Japan, whither he had been sent from Goa, for the affairs of that new Christianity. And both of them, not long after, carried the holy corpse along with them in the vessel of Lopez de Norogna.
The ship was so old and worn, and out of all repair, that none durst venture to embark upon her. But when once it was divulged, that it was to carry the corpse of Father Francis, every one made haste to get a corner in her, not doubting but there they might be safe. And the passengers had no cause to repent them of their confidence; for, in effect, God delivered them, more than once, miraculously from shipwreck.
A furious tempest, almost at their first setting out, cast them upon banks of sand, and the keel struck so far into it, that they could not get her off; when, against all human appearances, the wind coming about, and blowing full in their faces, disengaged the vessel; and, that it might manifestly appear to be the hand of God, the blast ceased that very moment when the keel was loosened from the sands.
Not long after, at the entry into the gulph of Ceylon, they struck impetuously against some hidden shelves, the rudder flying off with the fury of the stroke, the keel stuck fast within the rock; and it was a miracle that the vessel, being so crazy, did not split asunder. The mariners did that on this occasion, which is commonly put in practice in extremity of danger: They cut the masts with their hatchets, but that being of no effect, they were going to throw all their lading overboard, to ease the ship; but the fury of the waves, which beat upon her on every side, and outrageously tossed her, suffered them not to perform what they desired. Then they had their last recourse to the intercession of that saint, whose corpse they carried. Having drawn it out of the pilot's cabin, they fell on their knees about it with lighted flambeaux; and, as if Father Xavier had been yet living, and that he had beheld and heard them, they begged succour of him from that eminent destruction.
Their prayer was scarcely ended, when they heard a rumbling noise from underneath the vessel; and at the same time, perceived her following her course in open sea: from whence they concluded, that the rock was cleft in pieces, and had left a free passage for the ship.
They pursued their voyage cheerfully; and turning towards the cape of Comorine, landed at Cochin. The whole city came to pay their last duty to their instructor and beloved Father; and it is incredible what demonstrations of piety the people gave. From Cochin they set sail for Baticula. The wife of Antonio Rodriguez, one of the king's officers, who had long been sick, was in hope to recover, if she could see Father Francis. She caused herself to be carried to the ship, and at the sight of the dead saint, was restored to her health at the same moment. Not satisfied with this, she was desirous to have a little piece of the cope, with which the Father was habited; and it is wonderful what cures she effected by that precious relique.