Indeed to apply it to the true Roman Church, or the right succession in the Apostolic see, which was in the days of S. John, or in the time of the Christian Emperors, it were both folly and blasphemy: but to apply it to the Church of Rome, and counterfeit succession of Popes, it is wisdom and holiness. For Saint John Prophesies not only of the cruelty of the earthly estate of that city, but also of the false prophet and antichrist, which should usurp an ecclesiastical state and dignity in that city. The church of Rome indeed was one thing, and Babylon in Rome was another thing, while the Church of God was at Rome, and was persecuted by the heathen Emperors. But when the Emperor of Rome was Christian, one of the heads of the beast was wounded to death, as c. 13. even that sixth head, which was the persecutor in the time of Saint John: But this head was healed in Constantius the heretic Emperor, Valens, and Julian the Apostate, etc. and still the seventh head was to come, But great preparation was made for him, while the Bishop of Rome grew beyond the limits of a Christian Ministry, into foreign and heathen dominion as Socrates testifies, Bk. 7. chapter 11. in the time of the Christian Emperors, And when the mystery of iniquity wrought not so closely in that see, but the forgery of the Bishops was discovered in the African Council, unto which they obtruded a counterfeit Canon of the Council of Nicea for their primacy. And while Leo, Bishop of Rome, will not obey the decree of the general Council of Chalcedon, which gave equal privilege of dignity to the Bishop of Constantinople, which was new Rome, with those which the Church of Rome before had claimed as peculiar to her alone (sess. ultim). In the best and most Christian times of Rome therefore, when the head of the Heathen Empire was wounded to death, it was counted of the ancient Fathers to be Babylon here spoken of, because of the seventh head which is the Kingdom of Antichrist, that was looked for, to come in place of the sixth head, which was the earthly state of heathen, heretical, and persecuting emperors: Therefore not the true Church in Rome, but Rome the persecutor of the saints, first in the heathen and heretical emperors, afterward in the proud popes, and the kings subject to them, is Babylon the mother of all abominations.
Thomas Cartwright, A Confutation Of The Rhemists Translation, Glosses And Annotations On The New Testament (1618), 742.