St. Peter's in Rome...destroyed and missing, with PeterAnd I will give unto my two witnesses, and they shall prophesy a thousand two hundred sixty days, clothed in sackcloth. These are the two olive trees, and the two candlesticks, that stand before the Lord of the earth. And if any man will hurt them, fire shall come out of their mouths, and shall devour their enemies. And if any man will hurt them, in this manner must he be slain.
These have power to shut heaven, that it rain not in the days of their prophecy: and they have power over waters to turn them into blood, and to strike the earth with all plagues as often as they will. And when they shall have finished their testimony, the beast, that ascendeth out of the abyss, shall make war against them, and shall overcome them, and kill them. (Apocalypse of St John 11:3-7)
Where is the papacy here?
The court of God's temple clearly refers to St. Peter's in Rome. St. Peter's is the Temple of God, the place where the holiest relics of Christendom rest, the place where God decided to found His Church after the triumph of His Bride over the pagan Roman Empire.
We are told that St. Peter's would be trampled on "by the nations" for 42 months. Two witnesses appear simultaneously to prophesy and preach the word of God. They can perform miracles and impose plagues. The earth hates them because they testify to their sins. They are the leaders of the Church in exile. These witnesses are sent by God because there is no pope on earth who can act on His behalf.
The Beast, the Anti-Christ, kills the Two Witnesses at St. Peter's in Rome. Their bodies are kept in the open without proper burial. The world rejoices at the death of the Two Witnesses as the Anti-Christ occupies St. Peter's. God resurrects the two witnesses and they ascend to heaven.
It is clear that these events occur at a time where the world hates the Catholic Church to the point where Vatican City can be invaded and people will celebrate. The pope will likely be killed, there will be the forcible prevention of the election of a new pope or there will be an invalid pope who gives his authority to the beast.
Whatever scenario occurs it is clear that the Church will be leaderless for at least 42 months while the Devil enthrones himself in the Temple of God on earth. The leaders of the Church, the Two Witnesses, are not popes in the traditional sense. They are selected by God in a miraculous way because something terrible has happened to the papacy.