The Three Days of Darkness prophecy is a figurative description of the same event described in Apocalypse 11 (specifically Apoc. 11:11) and other places. There you will find the description of the period of the Two Witnesses, which says:

11 And after three days and a half, the spirit of life from God entered into them. And they stood upon their feet, and great fear fell upon them that saw them. 12 And they heard a great voice from heaven, saying to them: Come up hither. And they went up to heaven in a cloud: and their enemies saw them.

The same description is found in the Magisterial teaching in the Catechism of the Catholic Church (Section 677) which says:

677 The Church will enter the glory of the kingdom only through this final Passover, when she will follow her Lord in his death and Resurrection. The kingdom will be fulfilled, then, not by a historic triumph of the Church through a progressive ascendancy, but only by God's victory over the final unleashing of evil, which will cause his Bride to come down from heaven. God's triumph over the revolt of evil will take the form of the Last Judgement after the final cosmic upheaval of this passing world.

The key takeaway is this: the Church, in the End Times, will go through a process similar to Jesus's Passion, Death, and Resurrection. In other words, it will look like all is lost for the Catholic Church, just as it did for Jesus after his public ministry had ended. But in the end of her ministry, the Church will undergo a miraculous resurrection of her own. So don't lose heart. Keep the candle of faith burning in your heart during this time of trial. If you do this, you will have your reward.