In the mean time, all the Portuguese vessels, excepting only the Santa Cruz, which had not yet her whole lading, set sail from Sancian for the Indies.  Xavier gave many letters to the merchants, to be delivered both at Malacca and at Goa.  He wrote to his friend James Pereyra, in terms which were full of acknowledgment and charity.  “Almighty God,” said he in his letter, “abundantly reward you, since I am not able of myself to do it; at least, while I continue in this world, I shall not fail to implore the Divine Goodness to confer on you, during your life, his holy grace, accompanied with perfect health, and after your death eternal happiness.  But as I am persuaded, that I cannot acquit myself, by these my prayers, of the great obligements which I have to you, I beg all those of our Society in the Indies, to desire of God the same blessings in your behalf.  For what remains, if I compass my entrance into China, and if the gospel enter with me, it is to you, next to Almighty God, to whom both the Chinese and myself shall be owing for it.  You shall have the merit of it in the sight of God, and the glory in the sight of men.  Thus, both the Chinese, who shall embrace the faith, and those of our Society, who shall go to China, shall be obliged, to offer, without ceasing, their vows to heaven in favour of you.  God grant us both the happiness once to meet in the court of China!  As for myself, I am of opinion if I get into that kingdom, and that you come thither, you will either find me a prisoner at Canton, or at Pequin, which is the capital city of that empire; and I beseech the Lord, out of his infinite mercy, that we may be joined together either in the kingdom of China, or at least in the kingdom of immortal glory.”

He wrote by the same conveyance to Father Francis Perez, superior of Malacca.  He commanded him, in virtue of holy obedience, to depart with the soonest out of that unhappy town, and to conduct his inferiors to Cochin, where he established him rector of the college, in the place of Antonio Heredia, whom he sent to Goa.  Though Father Xavier deplored anew, the wretched condition of Don Alvarez, it hindered him not from enjoining Father Barzaeus, in his letter to him, that he should work the bishop to send his orders to the grand vicar of Malacca, therein declaring the governor to be excommunicated.  And he took this way, not only because hardened and scandalous offenders, such as Don Alvarez, ought to incur a public dishonour, by that means to induce them to a serious consideration of their own estate, and that others might take warning by them; but also, that succeeding governors might fear, by the example of his punishment, to set themselves in opposition to any intended voyage of the missioners, who should be sent hereafter to the Moluccas, Japan, or any other places.

He desired Father Barzaeeus, in the same letter, to receive few persons into the Society, and to make an exact trial of those whom he should receive:  “For I fear,” said he, “that many of them who have been admitted, and daily are admitted, were better out of our walls than within them.