6 How, then, you will say, do we read in the apocalypse written by John: “The beast that ascends out of the bottomless pit shall...kill them [that is, obviously, the prophets], and their dead bodies shall lie in the street of the great city which spiritually is called Sodom and Egypt, where also their Lord was crucified?” If the great city where the Lord was crucified is Jerusalem, and if the place of His crucifixion is spiritually called Sodom and Egypt; then as the Lord was crucified at Jerusalem, Jerusalem must be Sodom and Egypt.
Holy Scripture, I reply first of all, cannot contradict itself. One book cannot invalidate the drift of the whole. A single verse cannot annul the meaning of a book. Ten lines earlier in the apocalypse it is written: “Rise and measure the temple of God, and the altar, and them that worship therein. But the court which is without the temple leave out and measure it not; for it is given unto the Gentiles; and the holy city shall they tread under foot forty and two months.” The apocalypse was written by John long after the Lord's passion, yet in it he speaks of Jerusalem as the holy city.
But if so, how can he spiritually call it Sodom and Egypt? It is no answer to say that the Jerusalem which is called holy is the heavenly one which is to be, while that which is called Sodom is the earthly one tottering to its downfall. For it is the Jerusalem to come that is referred to in the description of the beast, “which shall ascend out of the bottomless pit, and shall make war against the two prophets, and shall overcome them and kill them, and their dead bodies shall lie in the street of the great city.” At the close of the book it is farther described thus: “And the city lies four-square, and the length of it and the breadth are the same as the height; and he measured the city with the golden reed twelve thousand furlongs.
The length and the breadth and the height of it are equal. And he measured the walls thereof, an hundred and forty and four cubits, according to the measure of a man, that is, of the angel. And the building of the wall of it was of jasper; and the city was pure gold” — and so on. Now where there is a square there can be neither length nor breadth. And what kind of measurement is that which makes length and breadth equal to height? And how can there be walls of jasper, or a whole city of pure gold; its foundations and its streets of precious stones, and its twelve gates each glowing with pearls?
Source: Letters (New Advent)