Leary to run counter this truth, they often attempt to deny the reality of facts or the obvious meaning of statements that apparently contradict this divine assistance.
They are thus caught in a seemingly dead-end dilemma: deny either the facts or the assistance of the Holy Spirit to the Church.
In the Church, the Holy Spirit Favors Good but Allows Evil to Occur
This is a false dilemma springing from a rather simplistic conception of the work of the Holy Spirit in the Church. One confuses “assistance” by the Paraclete, an effect of God’s special providence for His Church, with a direct government that replaces men or eliminates their free will.
However, that is not the way it works. Although Jesus Christ promised the help of the Comforter, He wanted the Church to be governed by men, who have special help from the Holy Spirit but who are not impeccable or exempt from temptations of the devil, the world, and the flesh.
Thus, although the Paraclete assists members of the hierarchy with special graces, that assistance does not eliminate their free will or the tendency to evil inherited with Original Sin.
On the other hand, one must keep in mind that this special action of Divine Providence favors good but also often allows evil to occur in the human element of the Church as a trial or as punishment for our sins.
Therefore, one cannot use the argument of the Holy Spirit’s assistance to the Church to justify deviation, recklessness or scandal, as if the evil were favored by the Divine will and not merely allowed.
God Allows Crises in the Church
Obviously, God does not want clear or sufficiently documented facts to be misrepresented by historians in an attempt to “save” the holiness of the Church.
Such an attitude would run counter to the truth and therefore the holiness of the Church and was severely condemned by Pope Leo XIII (1878-1903), who employed the inspired words of the book of Job (13:7): “God has no need of our lies.”
Indeed, the Pontiff emphasized, “The Church historian will be all the better equipped to bring out her divine origin, superior as this is to all conceptions of a merely terrestrial and natural order, the more loyal he is in naught extenuating of the trials which the faults of her children, and at times even of her ministers, have brought upon the Spouse of Christ during the course of centuries. Studied in this way, the history of the Church constitutes by itself a magnificent and conclusive demonstration of the truth and divinity of Christianity.”
When opening the Vatican Secret Archives to historians, the same Pope insisted: “Say nothing false, hold back nothing true.”
No one with a sufficient knowledge of Church history can deny the crises through which She has passed and the weaknesses and scandalous attitudes of many popes.
Thus, in his Encyclical Mystici Corporis Christi, Pope Pius XII (1939-1958) explains that due to our inclination to evil, “at times there appears in the Church something that indicates the weakness of our human nature.” “That regrettable inclination to evil,” he says, is manifested “even at times in the most exalted members of His Mystical Body.” However, he adds that God allows this to happen “for the purpose of testing the virtue of the Shepherds no less than of the flocks, and that all may increase the merit of their Christian faith.”
This is the reason why Catholic historians such as Ludwig von Pastor, whose monumental History of the Popes was praised by Pope Leo XIII, did not hesitate to present excesses and scandals by popes in a clear and well-documented fashion.
Was it the Will of the Holy Spirit for Alexander VI to Be Elected?
No one can assume, for example, that the Holy Spirit, Who assists at Conclaves, wanted or favored the selection of Rodrigo Cardinal de Borgia, known to have fathered four children by his concubine Vannoza dei Cattanei and others by different women. Obviously, his election as Pope Alexander VI was simply a permission for the punishment of a mankind inebriated with Renaissance paganism.
Nor can one attribute to the Divine will the elevation to the papacy of Benedict IX (1032-1044), about whom historian Fr. Joseph Brusher S.J. comments: “A young man probably about twenty years old, [he] was a cleric. That was about his only qualification for the papacy. Unqualified by his youth, his bringing up, his depravity, Benedict IX became one of the very few really disreputable popes.” The Catholic Encyclopedia is more direct: “He was a disgrace to the Chair of Peter.”
We Should Always Distinguish Between the Divine Will and Permission
Once the distinction between the manifestation of God’s will and His mere permission is clear, it becomes obvious that the assistance of the Holy Spirit to the Church does not prevent infidelities and crises.
On the other hand, as we saw above in texts by Popes Leo XIII and Pius XII, far from countering the holiness of the Church, such infidelities and crises emphatically show how only an institution of Divine origin could last forever despite human weakness and the tendency to evil inherited with Original Sin.
But even during Her worst crises, thanks to the assistance of the Holy Spirit, the Church never failed to sanctify through the sacraments or to present the truth even though, at times, Catholics had to make a great effort to remain faithful, as for example, during the Arian crisis.
Confide in Mary Most Holy, Who Crushed All Heresies
The present crisis ─ an extension of the one caused by the modernist heresy that Saint Pius X denounced ─ is now reaching such a climax that many feel discouraged.
At the highest levels of Church leadership, the possibility of giving Holy Communion to people objectively in the state of mortal sin is being discussed; and some even see, in homosexual relationships, “gifts” useful to Christianity.
A better understanding of the assistance of the Holy Spirit is required. It is not only positive in the sense of boosting zeal for doctrine and the salvation of souls – which the Church always promotes in one way or another—but also allows evil to occur in order to test us and punish the sins of mankind.
Just as the faithful, following the example of bishops like Saint Athanasius and Saint Hilary of Poitiers resisted the tremendous crisis of Arianism, we too, certain of the help of Divine Providence, must resist “strong in faith” (1Peter 5:9).
More than ever, in this period of darkness and confusion, we must always resort to the intercession of Mary, who “alone has crushed all heresies.”
 Cf. E. Magenot, “Assistance du Saint-Esprit,” Dictionnaire de Théologie Catholique (Letouzey et Ané, Paris, 1931), v. I, deuxième partie, cols. 2123-21-27.
 Cf. R. Garrigou-Lagrange, “Providence, Théologie, L’Infalibilité,” Dictionnaire de Théologie Catholique, v. XIII, première partie, col. 1015.
 Pope Leo XIII, Encyclical Depuis Le Jour, On the Education of the Clergy, Sept. 8, 1899, nn. 25-26. Available at http://w2.vatican.va/content/leo-xiii/en/encyclicals/documents/hf_l-xiii_enc_08091899_depuis-le-jour.html
 Brief Saepe numero, Aug. 28, 1883.
 Pope Pius XII, Encyclical Mystici Corporis Christi, On the Mystical Body of Christ, June 29 1943, n. 66. Available at http://www.vatican.va/holy_father/pius_xii/encyclicals/documents/hf_p-xii_enc_29061943_mystici-corporis-christi_en.html
 Cf. Ludwig Pastor, The History of the Popes, (Herder, St. Louis, Mo., 1923) v. 5. pp. 363-364.
 Joseph S. Brusher S.J., Popes Through the Ages, (D. Van Nostrand Co., Toronto-New York, 1959) p. 292.
 H. Mann, sv. Pope Benedict IX, The Catholic Encyclopedia, (New York: Robert Appleton Co., 1907). Available at http://www.newadvent.org/cathen/02429a.htm.
 When one says that God permits evil, it must be clearly understood that this is never a positive permission, such as that of a father who allows his son to frequent a place of perdition. It is only a negative permission, that of not employing extraordinary means to prevent evil from occurring.
 “Rejoice, O Virgin Mary, for alone thou hast put an end to all heresies” (Office of the Blessed Virgin Mary).