Zach posted a series of articles (here, here, here, and here) from early Church history into the middle ages. While I found the first article agreeable, it is clear that he is painting a Reformed interpretation of Church history. In my patient waiting for him to complete his series I have been able to do some research and provide a bit of a fact check on the narrative he put forward. In this first article I will simply be responding to some of the logical jumps Zach makes that aren’t merited. In my next article I will explain why Apostolic Succession, though it was defined in a much less clear way in the early Church, is the only continuity we Christians today have with the Apostles. In my third article I will focus specifically on scriptural evidence that continuity of the Church through the apostles and their chosen successors was exactly what Christ wanted.
Here is a list of claims by Zach that I am going to be arguing against.
“While the church had previously dealt with these issues by internal debate, they were now set as official doctrine, an act that would alienate the “true” church from other professing “Christians.” This trade-off kept the church from the internal division along doctrinal (and, perhaps, cultural-racial) lines that largely characterized the church as early as Paul, but it also became the first time that the church found itself rejecting others in a unified, well-defined fashion. In finding its own shape, the church had to set its own boundaries and limits.”
To specify, Zach seems to be implying without directly stating that the early Church did not have internal discussions that resulted in heresy being declared and former members of the Church who persist in heresy being cut off. Needless to say, this is mostly false.
In the Church before the first ecumenical council, various authors fervently combated heresy. It should be noted that the first heresies were not concerning the nuances of Christ’s divinity; this was still to be determined. Instead there were two groups of conflict in the early Church: the defenders of Apostolic Authority (aka proto-Orthodoxy) and the Gnostics. The two earliest writings on heresy in the early Church (before Constantine, mind you) were by St Ireneaus and Tertullian. They both fervently argued that schism and dissension are not good things.
Ultimately the Gnostics rejected the evangelical tenor of Christianity in favor of a more secretive religion, where only those with correct knowledge of Christ and theology would be saved. In contradiction to the wider Church in which various theological discussions and disagreements were had, the Gnostic outlook was one of black and white, material and spiritual, making it much more dualistic than Christianity is today. Gnosticism focused on the individual being as the center of theological inquiry and discernment, rather than the community. Without recognizing the legitimacy or authority of the broader church, Gnosticism became one of the earliest heresies to threaten the spread of the Gospel. Ultimately it was first ecumenical councils that ended Gnosticism as a serious force, yet these decisions are rooted in the Synods of Antioch (Pre-Constantine: 264-269 AD), and ultimately the writings of Church fathers before that. 
“This communication was between two elites: the Pope and the Emperor. Those high up in the church hierarchy were now high up in society. The poorer local priests did not necessarily stand with the archbishops and popes who represented the higher ranks of the church. The drama that took place between church and state became largely removed from the Christian masses and those ruled by the state.”
Again, it would seem Zach is implying here that the role of the Pope, or Patriarchs generally, was not spiritual but just squabbling among the elite. Further, he seems to imply that local priests did not listen or stand with their superiors. This is where the office of the Pope becomes important. The Pope, like all Christians, is part of the body of the Church. Conflict, squabbling, and sin are not foreign to Bishops, and much of this conflict did take place far away from the daily lives of most Christians.
However, the office of the Bishop and the authority of that office came into direct contact with the faithful on a daily basis. The earliest orders of monks, who kept the continuity of Christianity strong in an unruly age, answered to their local Bishop. Those who wanted to study theology, be ordained, and preach, did so with the approval of the episcopate. In the west, the various monastic orders and parishes were subject to the office of the Bishop of Rome.  From issues of fasting to manners of celebrating Easter, the role of the Bishops was central in the life of the faithful Christian.
“Traditionally, the investiture of bishops was a privilege of the Holy Roman Emperor, but Pope Gregory issued a papal decree that offered reforms for this system, taking away the Holy Roman Emperor’s ability to install bishops.”
This claim, one of many in Zach’s third article, is once again not incorrect but seems to imply falsehoods on which his later narrative is built. Namely a narrative that the institutional Church became primarily political, rather than religious. While the Holy Roman Emperor, and other noble families throughout Western Europe, did nominate Bishops, it is hardly something that can be called a tradition. It did not apply to the universal Church, and was only a few hundred years old at the time of the controversy.
Further, it can be argued in an age where it took weeks to months to communicate, local Lords and Nobles would know their lands and peoples best to know which individuals may make the best Bishop. There is a strong argument from subsidiarity that the King, who is given his right to rule from the Church, would be in the best position to nominate Bishops in his Kingdom. As history shows, this practice succumbed to human corruption (big surprise), yet hindsight is 20/20 and one can understand the theoretical merits of local investiture of Bishops.
Regardless, the main gist of the article was to build a case that the office of Bishop became (or was always) primarily political. While politics has always influenced the Church, from the corruption among the Apostles to Vatican scandals, the office of the Apostles is something that is primarily religious, with God as its safeguard.  
“The local churches that had largely been suppressed and silenced finally broke out in full opposition to the authority that held them in their smoldering position for centuries. And thus it was revealed that the “church” had never truly been represented well by the papacy, that the “church” was a difficult reality to maintain, one that required an enormous amount of power, because it was truly more of a concept than a reality. The church was composed of many local churches, and the alienation of those with strong disagreement proved to be an unsustainable practice. So the power of the autocracy of the papacy was split partially to the tyranny of the majority that often took over in Protestant circles.”
This quote, like many in Zach’s article, paints a dubious picture that the focal point of the Reformation was between local parishes and Church hierarchy. While some parish priests did break away from the Church, the mere existence of these incidents does not make a larger trend. The Reformation period was a chaotic free-for-all that ensued once Luther questioned the authority of the Church and political leaders sought advantage from it. In Germany princes used the Protestant movement to establish their own political power in the Holy Roman Empire. In Denmark, Norway, and England the State forcibly inserted their own bishops and persecuted the local parishes that held true to the Catholic Church. Lutherans condemned Calvin, who condemned the reformer Servetus, who was ultimately burned at the stake by Geneva reformers.
Zach’s narrative assumes the parish is a church in which the priest and his congregants represent a similar theology that would be different from another parish. In reality, priests moved around from parish to parish. Geography brought people together to celebrate Mass, not theological beliefs. For the most part, the Reformation happened at a higher ecclesiological level with bishops leaving the Church and the local parishes, when protesting their Bishops apostasy, were crushed by the state.  There are very few cases of individual parishes switching from Catholicism to Protestantism. This only happened with Calvin and similar reformers who were opposed by other Protestants and Catholics alike. The division of the reformation was not the papacy from the parish, or even the Bishops, but from each other. The reformation was the chaotic result of individuals who rejected Church authority and the political actors who sought to use this rejection to their advantage. 
As I finish this article, I will recognize many of my points are negative; I am pointing out flaws in Zach’s narrative rather than building my own argument. In the next two posts I will go through and define where I see the key root of disagreement: Apostolic Succession. This post was fun to write but, honestly, given the breadth of history, so much more could be said on each of the points I made. Nevertheless life, and I, am finite and I hope I was able to clearly put forward what I saw to be problematic in Zach’s posts!
 Arguably Christ is the first to object to Gnostic heresy in his command to the first Christians to go forth and preach the Gospel to all people. Obviously, a Gnostic would take issue with this statement. For reading on Gnosticism read the Catholic Encyclopedia and the Internet Encyclopedia of Philosophy pieces on the topic. For reading on the response of the Church to Gnosticism, Irenaeus gives the most thorough here.
 While this example is just one, it illustrates the common understanding that those in the Western Church, even the Celtic barbarians in Britannia, would not “contradict the decrees of him [Representatives of Rome] who keeps the doors of the Kingdom of Heaven, lest he should refuse me admission.”
 Corruption of the Apostles refers not only to Judas’ betrayal but to Peter’s denial, the Apostles’ debating on who would be first into the kingdom of heaven, and the clashes between Peter and Paul. The protection of Apostolic Succession by God is something made clear in Matthew 16:17-20.
 Zach’s third article also addresses Papal Power and the debates around how far it should extend. Of course, this is a debate worth having within Apostolic Churches, but given Zach’s Protestant theology, I think it is safe to say he is not arguing for an Orthodox position here.
 This is not to say that Catholics didn’t crush Protestants when they had control over the state; it’s simply to say that everything during the Reformation was painfully political.
 For a concise history of Reformation events from the Catholic (historical) perspective, this link is very useful.