He did not wait long to exercise his power, and in 1641, to the consternation of everyone, he flung out of office no less a personage than the viceroy himself who was universally esteemed for his upright and virtuous life. By this extraordinary act, Palafox became practically viceroy and captain general, while retaining his ecclesiastical dignities. In a few months, however, the new viceroy, Salvatierra, arrived. Palafox was soon to clash with him also, by blocking all the official work of the audiencia; holding up despatches, delaying decisions, absenting himself from the city, etc. For five years complaints against him poured into Spain but without effecting any change. Salvatierra even accused him of malversation in office, particularly in its finances and added that his whole occupation seemed to consist in writing the Life of St. Peter. His ecclesiastical government was no less disorderly. To gain the favor of those around him he transformed the Indian missions into parishes and put them in charge of priests who were absolutely ignorant both of the habits and language of the natives. The motive back of this change was that as mere mission posts the Indian settlements paid no tithes.
During all this time he continued to proclaim himself a friend of the Jesuits, but in 1641 when a canon of the cathedral wanted to make over a farm to the College of Vera Cruz, he was forbidden to do so under pain of excommunication unless the property was made subject to tithes. When the canon submitted the case to the audiencia he of course, lost it, because Palafox was the visitor of that tribunal. A further appeal was then made to the council of the Indies, but after two years of litigation the case was dropped without a decision. In the course of this contest, Palafox wrote in his plea that the Jesuits were enormously wealthy, while the cathedral of Puebla was destitute of resources. When Father Calderón refuted these assertions, the bishop was wrought up to fury and laid down as a diocesan rule that, under pain of excommunication, no property transfers could be made to religious orders unless this tithe clause was inserted, and he enjoined that the sick and dying should be admonished of that censure. He followed this up by sending an order to all the Jesuits to deliver up their faculties for inspection within twenty-four hours, under penalty of excommunication. Their reply was that they would have to refer the matter to the provincial. This was, according to Astrain, a grave act of imprudence on the part of the Fathers, and such, later on, was the ruling of the Roman Congregation and of the Pope himself.
Of course, in the rigor of the law the bishop had an absolute right to demand the faculties of all the priests of his diocese, but in the concrete it is hard to blame the action of the Fathers in this instance. They did not refuse, but merely wanted time to lay the case before their superior. Moreover, the action of the bishop was altogether out of the ordinary. Up to that time, his own confessor was a Jesuit, and faculties had been issued by the bishop to several others of the Society; during his incumbency he had employed them in various missions of the diocese, he had invited them to preach in his cathedral; and, indeed, they had been using their faculties to confess and preach ever since 1572. It is true that some of their original privileges had been modified or curtailed, but in these two principal functions no radical change had been made. Might they not then have thought that, in view of what the bishop had already done both in civil and ecclesiastical matters, he was mentally deranged? The average man of the world would have arrived at that conclusion.
At all events, the faculties were not forthcoming within the twenty-four hours, and all the Jesuit priests of Puebla not only found themselves dishonored and disgraced by being held up to the people as excommunicated, but by this act of the bishop doubt was thrown upon the validity of all the absolutions they had given in the administration of the sacrament of Penance. Astrain tells us that Father Legaspi attempted to preach in the Jesuit church, and when forbidden to do so by a messenger from the bishop's palace, refused to obey, but apart from the fact that this would be in absolute contradiction with the traditional instincts and training of any Jesuit, Astrain himself relates in the following chapter that the Roman Congregation which examined the whole miserable quarrel decided that Legaspi's sermon was delivered before and not after the prohibition. Recourse was then had to a privilege accorded to the Spanish colonies of constituting a commission of judges to consider and decide the case. This also was subsequently condemned by the Roman Congregation and by Innocent X, but on the other hand, communication with Rome was difficult in those days, and the course entered upon was taken with the approval of the heads of other religious orders, of the viceroy and of the cabildo or mayor. It is true that efforts should have been made to placate the angry prelate, but the documents show that the most humble supplications had been made to him only to be repulsed with abuse.
It would have been futile to refer the case to the audiencia, for Palafox controlled it absolutely. Moreover, it was urged that the plea presented to the commission did not regard merely the wholesale suspension and excommunication, but other grievances as well. There were twenty-nine in all. The commission brought in a verdict against the bishop, but he refused to recognize the authority and even excommunicated the members of the court who, with what Father General Caraffa described as an "exorbitancia grande," had excommunicated the prelate. Then the whole city was in an uproar and Palafox rode through the throngs of the excited populace conjuring them to keep the peace, but at the same time preventing it by proceeding to the cathedral, and, amid the most lugubrious ceremonies and in full pontificals, excommunicating all his opponents. The Mexican Inquisition now intervened and enjoined silence on all parties. Salvatierra, the viceroy, also helped to quell the disturbance. Nevertheless, on June 6, Palafox issued another proclamation declaring that his enemies had been assembling arms in their houses, and were bent on getting control of the country. He again made a public appearance in the streets of Mexico, but two days afterwards he submitted the whole matter to the viceroy.
Salvatierra then implored him with the greatest respect and kindness to restore tranquillity and peace to the distracted colony, but on June 15, Palafox disappeared from the city; and no one knew whither he had gone. It was officially reported later on, that he had betaken himself first to the hacienda of Juan de Vergus, but after two days had disappeared again. For two months his whereabouts could not be ascertained, but in a letter to the Pope, he described himself as wandering for ten days in the forest and mountains without shelter or food, and exposed to death from serpents and wild beasts. He called himself another Athanasius. Finally he returned to the original hacienda and remained there until November. Before his departure, he had empowered the cabildo to have the diocese administered by three ecclesiastics whom he designated; but one of them was imprisoned by the viceroy, and the two others refused to serve. Whereupon, the cabildo called a meeting at the city hall. Alonzo Salazar de Baraona presided and the Jesuits were ordered to display their faculties, which they did; they were then declared rightful ministers of the sacraments.
During his retirement Palafox had received two letters from Spain, one deposing him from his office of visitor, and another announcing the transfer of Salvatierra to Peru. The first was the reverse of pleasant, but the second was a source of great satisfaction for, if we are to believe Salvatierra, Palafox had aspirations for the viceregal office. Possibly with that in view, he willingly assented to the conditions on which he was to be allowed to re-enter his diocese, namely to regard as binding all that had been done in his absence. It was fully nine months before Salvatierra left Mexico, and during all that time there was peace in Puebla; but hostilities were resumed immediately afterwards. Palafox refused to be bound by his contract with Salvatierra; he declared the acts of the commission to be null and void, reasserted the invalidity of the Jesuit faculties, and put three of his own canons in jail. In September, he received a brief from the Pope which he regarded as a justification of all that had been done. In the main, the document asserted the fundamental right of the bishop to examine the faculties of the priests and condemned the proceedings of the commission. Whereupon twelve of the Fathers submitted their faculties to the bishop. But that did not satisfy him. He insisted on the Jesuits appearing in public in a penitential garb, as at an auto-da-fé, and receiving from him a solemn absolution from their excommunication. He also made it a matter of confession for the faithful to have been absolved by Jesuits or to have listened to their sermons.
From this odious ruling an appeal was taken to the royal council; whereupon Palafox despatched three letters to the Pope. The first was about the parochial rights of the other religious orders; the second complaining of the silver mines, vast haciendas and wealth of the Jesuits, and the third consisting of fifty-eight pages of the most atrocious calumnies ever written by a Catholic, and asking finally that they should be made like other religious orders with choir, cloister, etc. Ten years later, the General of the Discalced Carmelites inquired of Palafox why he wrote these letters. "I did so," he says, "because I was incensed against the Jesuits for not treating me with proper respect, but I am surprised that I have lost their affection and was not aware of it till now." At last, wearied of it all, Philip IV ordered him to return to Spain immediately, but he obeyed in a very leisurely fashion. In Rome, the case dragged on for four more years and finally a verdict was rendered affirming among other things that the Fathers had been properly provided with faculties, and had ceased to preach and hear confessions when ordered to do so. The only censure they received was for having convoked the commission to judge the case in the absence of the bishop. The trouble had lasted for sixteen years, but it created a deep prejudice against the Society a century later.