The Physical Refuges
The Church will be reduced in its dimensions, it will be necessary to start again. However, from this test a Church would emerge that will have been strengthened by the process of simplification it experienced, by its renewed capacity to look within itself… the Church will be numerically reduced. —Cardinal Ratzinger (POPE BENEDICT XVI), God and the World, 2001; interview with Peter Seewald
The truth is that, were it not for God's providence, the Church would be decimated were the Antichrist to have his way. But God will protect His people, not only spiritually, but physically—and this according to Scripture, Tradition and prophetic revelations. Indeed, said Paul VI:
It is necessary that a small flock subsist, no matter how small it might be. —POPE PAUL VI, The Secret Paul VI, Jean Guitton, p. 152-153, Reference (7), p. ix.
Early Church Father, Caecilius Firmianus Lactantius (250-317 A.D), foresaw with great precision what this future period would look like… and when the faithful would eventually flee to sacred refuges:
That will be the time in which righteousness shall be cast out, and innocence be hated; in which the wicked shall prey upon the good as enemies; neither law, nor order, nor military discipline shall be preserved… all things shall be confounded and mixed together against right, and against the laws of nature. Thus the earth shall be laid waste, as though by one common robbery. When these things shall so happen, then the righteous and the followers of truth shall separate themselves from the wicked, and flee into solitudes. —The Divine Institutes, Book VII, Ch. 17
After the Warning, there will form two camps: those who accept the grace to repent, thus passing through "the door of Mercy"… and those who will harden their hearts in their sin, and thus, be destined to pass through "the door of Justice." The latter will form that camp of the wicked who, for “forty-two months”, will be “allowed to wage war against the holy ones and conquer them” (Rev 13:7). But according to Scripture and Tradition, a remant will be safeguarded:
…the woman was given the two wings of the great eagle, so that she could fly to her place in the desert, where, far from the serpent, she was taken care of for a year, two years, and a half-year. (Rev 12:14)
The precedent for this physical protection is in the Gospel of Matthew:
And having been warned in a dream not to return to Herod, [the magi] departed for their country by another way. When they had departed, behold, the angel of the Lord appeared to Joseph in a dream and said, “Rise, take the child and his mother, flee to Egypt, and stay there until I tell you. Herod is going to search for the child to destroy him.” Joseph rose and took the child and his mother by night and departed for Egypt. (Matt 2:12-14)
The Book of Maccabees, which many believe is a "template" for the coming persecution and Passion of the Church, notes the Jews flight into refuges:
The king sent messengers… to prohibit holocausts, sacrifices, and libations in the sanctuary, to profane the sabbaths and feast days, to desecrate the sanctuary and the sacred ministers, to build pagan altars and temples and shrines… Whoever refused to act according to the command of the king should be put to death… Many of the people, those who abandoned the law, joined them and committed evil in the land. Israel was driven into hiding, wherever places of refuge could be found. (1 Macc 1:44-53)
Bear the standard to Zion, seek refuge without delay! Evil I bring from the north, and great destruction. (Jeremiah 4:6)
The pinnacle of destruction is at the hands of Antichrist. But even then, God will preserve a remnant:
The revolt and separation must come…the Sacrifice shall cease and…the Son of Man shall hardly find faith on earth… All these passages are understood of the affliction which Antichrist shall cause in the Church… But the Church… shall not fail, and shall be fed and preserved amidst the deserts and solitudes to which She shall retire, as the Scripture says (Rev. Ch. 12:14). —St. Francis de Sales
The Spiritual Refuges
Yet, these are temporal places, that in and of themselves, cannot save the soul. The only refuge that is truly safe is the Heart of Jesus. What the Blessed Mother is doing today is leading souls to this Safe Harbour of Mercy by drawing them into Her own Immaculate Heart, and sailing them safely to her Son.
My Immaculate Heart will be your refuge and the way that will lead you to God. —Second apparition at Fatima, June 13, 1917
In revelations to Fr. Michel Rodrigue, the Eternal Father promises:
I have given Saint Joseph, My representative on earth as protector of the Holy Family, the authority to protect the Church, that is the Body of Christ. He will be the protector during the trials of this time. The Immaculate Heart of My daughter, Mary, and the Sacred Heart of My Beloved Son, Jesus, with the Chaste and Pure Heart of Saint Joseph, will be the shield for your homes and for your family, and your refuge during the events to come. —from the Father, October 30, 2018
Most importantly, our Mother Church is and always will be our refuge from the gates of Hell. For she is built by Christ upon the rock of Peter's faith and safeguarded by Our Lord's promise to remain with His Church until the end of time.
The Church is thy hope, the Church is thy salvation, the Church is thy refuge. —St. John Chrysostom, Hom. de capto Euthropio, n. 6.; cf. E Supremi, n. 9
Last, pray Psalm 91, the psalm of refuge!
Read The Refuge for Our Times by Mark Mallett to understand the centrality of the spiritual refuge as opposed to physical refuges, and how survivalism is not the mindset of the Christian, but Heaven.