By the third century, a shift took place as the bishops of each Roman province formed the habit of meeting in a provincial synod, presided over by the bishop of the capital city, meaning the metropolitan bishop or archbishop. In the fifth century, the hierarchical evolution of Church government would be complete with the universal recognition of the Bishop of Rome. In the Catholic Church, these leadership groups assumed a somewhat different form over time. From the first, three orders were thought to stand by themselves, these being bishops, presbyters (or priests), and deacons, and these were the only orders considered necessary to a church. By the third century, a number of other orders were introduced, all lower than that of deacons and so called "sub-deacons," those who helped the deacons in the care of the poor and with the property belonging to the church, including the "acolytes" who lighted the lamps, and assisted in the celebration of the sacraments; the "exorcists" who cared for persons suffering from afflictions resembling the possession by devils; the "readers" who read the Scriptures in church; and the "doorkeepers." All these were viewed as belonging to the clergy. There were also women members of the clergy called deaconesses, employed among Christians of their own sex for such works of mercy and instruction as were considered not fit for men to do. This order did not last long. As for bishops, it was found convenient for the government of the Church that some of them should be placed higher than others. Meetings at which such things wee decided were called "synods" or "councils" and were eventually held once or twice a year. The bishop considered the leader in each area was called a "metropolitan" because each was bishop of the metropolis (or mother-city) of the country in which the council was held. These bishops were now seen as higher than their brethren. In time, it was considered natural that the bishops of very great cities should be considered as even higher than the ordinary metropolitans, and so thus the bishoprics of Rome, of Alexandria, and of Antioch, which were the three greatest cities of the empire, were regarded as the chief bishoprics and as superior to all others:

Those of Rome and Antioch were both supposed to have been founded by St. Peter, and Alexandria was believed to have been founded by St. Mark, under the direction of St. Peter. Hence it afterwards came to be thought that this was the cause of their greatness; and the bishops of Rome, especially, liked to have this believed, because they could then pretend to claim some sort of especial power, which they said that our Lord had given to St. Peter above the other Apostles, and that St. Peter had left it to his successors. But such claims were quite unfounded, and it is clear that the real reason why these three churches stood higher than others was that they were in the three greatest cities of the whole empire.

Rome would become the supreme center of power where the Pope would reside and rule over the whole of the Catholic Church, developing as well a hierarchy of offices and officers to aid in various ways, leading today to the central power in the Congregation of the Holy Office, which "publishes solemn decrees which clarify the Church's teaching or condemn some particular theory. The layman, by virtue of the bond of discipline, is in duty bound to pay heed to these decrees, but he may submit them to the judgment of his conscience and is permitted to criticize their premises as debatable. In matters of doctrinal interpretation the final word belongs, however, to the Church hierarchy and the Pope.."

It was in the fourth century that Pope Damasus I countered the claims of the Council of Constantinople by stating that the authority of Rome was not derived from a synodal decision but stemmed instead from Christ's commission to St. Peter (Matt. 16:18-19).

Church Government and Secular Government

The degree of secular control exercised by the Catholic Church has varied through history, depending in part on nature of the secular government of the time. The issue of what belongs to the Church and what should be left to secular government has often been raised and was addressed directly by St. Augustine. Augustine showed a Platonic duality in that he separated the secular from the sacred world in his image of the City of God, differentiated...

Each had its own important areas of concern. The City of Man is guided by self-interest, while the City of God is guided by divine love. In practical terms, Augustine draws a sharp distinction between secular and ecclesiastical authority. The best secular city is one where the secular authority is guided by divine Christian wisdom, and this becomes the ideal for the state in this world. It is an ideal not often reached, but it is the ideal to which human beings should aspire. In terms of government, Augustine considered the need for Christian rule of the Church over state. In order to have the ideal government, Augustine stated, secular law should co-relate to that of the Church. The purpose of the state is to promote peace and prosperity among the people, and it should also reflect only true religion. Government has the task of establishing commonly accepted rules for acquiring the necessities of life. Since God has doctrine over man, it follows that God has doctrine over state.
Augustine represented the Christian point-of-view of the time to the effect that "the secular state is rooted in iniquity, or at best only justifies itself by performing the duties of the police for the benefit of the righteous: the blunders and excesses of the later empire unduly discredited the possibilities of the secular state."

Augustine is seen as substituting his view of the state and politics for that of Cicero, whose view prevailed at the time, and in so doing "he removed the stipulation not only of a common sense of justice (consensus iuris) but also of a shared benefit or utility (communio utilitatis)."

Augustine saw government as a necessary control on earth, while the real power and guidance came from the City of god and not the City of Man. For Augustine, no government could create human happiness, and all that government could do was to place a limit on human evil by protecting the innocent and punishing the criminal. Government can perform its best effort by creating conditions on earth where the Church would be free to do its wok of brining people to God, for that is where human happiness really lies. As he writes in City of God,

For to this earthly city belong the enemies against whom I have to defend the city of God. Many of them, indeed, being reclaimed from their ungodly error, have become sufficiently creditable citizens of this city; but many are so inflamed with hatred against it, and are so ungrateful to its Redeemer for His signal benefits, as to forget that they would now be unable to utter a single word to its prejudice, had they not found in its sacred places, as they fled from the enemy's steel, that life in which they now boast themselves.

Augustine was reacting in part of the failure of Rome to achieve a true commonwealth, for he said that "it never had a just rule of law, applicable to a whole people." For Augustine, the study of these issues began with theology and an understanding of the City of God before the City of Man could be addressed.

At times, of course, the leadership of the Catholic Church has had considerable influence over secular affairs. It can be noted that in the thirteenth century, the nature of papal rule was such that he held a practically absolute position in Church government and even, in secular affairs:

The Pope was thought by most decretalists to enjoy the same absolute sovereignty over the Sacerdotium as the Lex Regia had granted to the Emperor in secular affairs. The scope of papal authority could be limited only by explicit provisions of divine and natural law and even there some canonists held that the Pope might exercise a dispensing power. In such theories of Papal supremacy the position of the general council was seriously depreciated, most decretalists holding that conciliar legislation possessed binding force only when underwritten by the Papacy.

Government and Protestantism

Protestantism necessarily shifted toward the City of Man for support of a different vision of the City of God because that was the only way to overcome the power of the government of the Catholic Church. The Catholic Church even before that had experienced opposition because its independence and self-sufficiency produced a good deal of anti-clericalism. It did more than that, however:

By an even stranger paradox it…