Msgr. Eugene Pacelli, the future Pope Pius XII:

“I am worried by the Blessed Virgin's messages to Lucy of Fatima. This persistence of Mary about the dangers which menace the Church is a divine warning against the suicide of altering the Faith, in Her liturgy, Her theology and Her soul. ‹…› I hear all around me innovators who wish to dismantle the Sacred Chapel, destroy the universal flame of the Church, reject Her ornaments and make Her feel remorse for Her historical past.

A day will come when the civilized world will deny its God, when the Church will doubt as Peter doubted. She will be tempted to believe that man has become God. In our churches, Christians will search in vain for the red lamp where God awaits them. Like Mary Magdalene, weeping before the empty tomb, they will ask, 'Where have they taken Him?'”

“I cannot reveal anything of what I learned at Fatima concerning the third Secret, but I can say that it has two parts: one concerns the Pope. The other, logically — although I must say nothing — would have to be the continuation of the words: In Portugal the dogma of the Faith will always be preserved.”

“In Portugal, the dogma of the Faith will always be preserved”: The phrase most clearly implies a critical state of Faith, which other nations will suffer, that is to say, a crisis of Faith; whereas Portugal will preserve its Faith.

‹…›

In the period preceding the great triumph of the Immaculate Heart of Mary, terrible things are to happen. These form the content of the third part of the Secret. What are they?

If “in Portugal the dogma of the Faith will always be preserved”… it can be clearly deduced from this that in other parts of the Church these dogmas are going to become obscure or even lost altogether.

‹…›

Thus it is quite possible that, in this intermediate period which is in question (after 1960 and before the triumph of the Immaculate Heart of Mary), the text makes concrete references to the crisis of the Faith of the Church and to the negligence of the pastors themselves.

‹…›

One conclusion does indeed seem to be beyond question: the content of the unpublished part of the Secret does not refer to new wars or political upheavals, but to happenings of a religious and intra-Church character, which of their nature are still more grave.

If in Portugal the dogma of the Faith will always be preserved, it can be clearly deduced from this that in other parts of the Church these dogmas are going to become obscure or even lost altogether. It is quite possible that the message not only speaks of a «crisis of faith» in the Church during this period, but also, like the Secret of La Salette, that it makes concrete references to internal strife among Catholics and to the deficiencies of priests and religious. It is also possible that it may imply deficiencies even among the upper hierarchy of the Church.

Moreover, how are we to understand Lucy’s great difficulty in writing the final part of the Secret when she has already written other things that were extremely difficult to put down? Had it been merely a matter of prophesying new and severe punishments, Sister Lucy would not have experienced difficulties so great that a special intervention from Heaven was needed to overcome them. ‹…› But, if it were a matter of internal strife within the Church and of serious pastoral negligence on the part of high-ranking members of the hierarchy, we can understand how Lucy experienced a repugnance that was almost impossible to overcome by natural means.

Cardinal Ratzinger in 1984 spoke of the Secret containing “dangers threatening the Faith”.[19]
Cardinal Oddi said to Italian journalist Lucio Brunelli on March 17, 1990, “It [the Third Secret] has nothing to do with Gorbachev. The Blessed Virgin was alerting us against apostasy in the Church.”[20]
Likewise Cardinal Mario Luigi Ciappi, who had been personal theologian to Pope John Paul II, said in a personal communication to a Professor Baumgartner in Salzburg, “In the Secret we read among other things that the great apostasy in the Church will begin at the top.”[21]

[19] Ibid., pp. 822-823. See also Jesus magazine, November 11, 1984.
[20] The Cardinal’s statement appeared in the Italian journal Il Sabato. Quoted from The Devil’s Final Battle, [Buffalo: Missionary Association, 2002], p. 33.
[21] See Father Gerard Mura, “The Third Secret of Fatima: Has it Been Completely Revealed”, Catholic, March 2002. Also quoted in The Devil’s Final Battle, p. 33.