Part 1 of this series focused on the cyclical mechanism that spiraled into the inevitable failure to maintain a coherent theology. Void of apostolic and prophetic revelation, that doom was inevitable. Before arriving at the marvelous restoration of the gospel and the relief from the various tensions created in the apostasy, it will be useful to focus on and understand exactly what those tensions were.
After nearly 1800 years without a prophet and revelation, Christian theology became a patchwork of contradictory ideas and philosophies. Language was subject to enforcement rather than inspection and when someone dared to examine it they risked the high charge of heresy and with it their property and often their life. So why would someone dare to broach a subject that could invoke the institution supporting it to ruin their lives? The answer is actually quite noble on most occasions - because the correctness of their worship was more important than the institution's control over it and they wanted to correct the institution.
So what tensions were worth risking life and limb over to correct? They primarily focused on the nature of the Godhead itself. There were also important doctrines and philosophies that were lost over time as the primary institutions excluded them for their inconvenience to the framework they were building. Most interesting in all of the iterations of doctrine, theology, and orthodoxy over the past two millennia is that the orthodoxy spent so much time and energy focusing on the first question of "Who is God" that they didn't spend much time answering the far more operative question that every member of humanity needs to know: how do we obtain salvation and what does the salvation we obtain even mean? Perhaps life is generally just so miserable that any notion of not being miserable was sufficient for the time, but obtaining that salvation is arguably the far more important question and yet the one with the most divergence and least amount of philosophy applied over the years to answer it.
Christian orthodoxy effectively poisoned the well by diverging from scripture and adding outside philosophies to it to resolve their problems. This can't really be helped - their options, without a prophet, were to either die on the hill of confusing and incomplete theology that couldn't stand up to the latest and greatest Greek philosophies, or adapt and overcome by accepting those philosophies into their framework. They chose the latter, and perhaps appreciation is owed for their continued struggle that brought Christianity forward in time, but without prophecy and revelation it was always a losing battle. The adoption of paganism only subdued the chaos to allow for growth, so let's examine that chaos.
The Resurrection and Incorporeal God Problem
Without irony, one of the original theologians to incorporate Plato into Christian theology was a man named Origen. Origen (185 - 255 AD), borrowing from Plato and somewhat matching his own Greek contemporary, Plotinus, created the inception of the pattern that would produce the illogic. One of the very first things he incorporated via that proto-Neoplatonism (cool word, I know) is the Incorporeality of God, which is to mean that God has no body or material substance. Immediately, this should be a problem for you if you believe that Christ is God, as He clearly has a body. Those who support the doctrine of the Trinity through this Catholic, Neoplatonistic lens, are forced to reconcile this notion, but it never gets clean, only abstracted.
As is the pattern, Catholics adopted Neoplatonistic vocabulary to encapsulate the tension, using "hypostasis" which means "foundation" or "underlying substance". The problem with this word is the same with homoousios - it wraps the concept without doing any work to disambiguate it. The new language, hypostatic union, attempts to hold two positions at once (much like how the trinity operates) by suggesting that Christ is both divine and has a body, despite bodies being not divine and despite not needing one. It produced some interesting heresies - combine Christ and His body too much in your language and straight to jail, not combine them enough and also straight to jail. While "straight to jail" draws on comedic popular culture, it's worth noting that it was an actual reality in both directions - Nestorius (386 - 451 AD) and Eutyches (378 - 456 AD) will attest. It created an even more interesting set of questions - If Christ is God and God is incorporeal - what is that body used for, is it just Christ's puppet, and why even get resurrected and put back on a dusty human body if God doesn't need it? To LDS theology the resurrection is a paramount step in paving the way for our eternal progression, but to many Christians it's seemingly a miracle with a confusing or at least incomplete explanation of purpose.
The various organizations that maintain this neoplatonism in their theology have explanations, but they are not consistent and rarely satisfying. The problems it creates infringe on both the accepted orthodoxy and the orthodoxy to come - notably the trinity.
The Two-Natures Problem
Because the Christian tradition formulated the Trinity to mean neither three entities nor one entity (while switching between describing both), there is no room for a fourth entity. This is a problem for the hypostatic union, because it essentially treats Christ as two beings which would increment the trinity to a quaternity - yet another heresy. So the orthodoxy has to enforce that Christ is one, while stating that he's two (or at least has two parts) and this creates a host of tensions with the new testament. The concept basically treats Christ's body as a puppet and undermines the most powerful thing He did for us - to suffer and die for our sins. If Christ's body isn't really Him and it's just some tool He uses, then it begs the question of whether or not He truly suffered for us or if it was just His marionette of a corpse that did so and if that has any meaning at all.
What's particularly striking about the language used to justify Christ's two parts - "natures" - is that that same language isn't used to justify the trinity, despite its potential to actually resolve the tensions in that situation. If the Godhead were three distinct, separate beings who all shared the same nature, making them one in that sense, then virtually all of the tensions with scripture are resolved - see the essay on the trinity and the LDS Godhead for a full examination.
The Divine Simplicity Problem
What's somewhat astounding about all of the tensions that the proto-neoplatonistic idea of Divine Simplicity creates is that Christianity doesn't actually need it in any sense. It was adopted in an attempt to understand, but its adoption wasn't necessary. You can whole-heartedly follow Christ and His examples, live every commandment, and give glory to God all without needing God to be divinely simple. Unitarians do this, but somewhat undermine Christ's divinity - the restored Gospel does it without undermining that divinity, precisely because it truly is the restored gospel of Christ. The problem is, once the bed was made, it had to be slept in. Early Imperial Christian theology began building their entire structure on this foundation and reverting it would be devastating, not only to the orthodoxy, but to the institution, as it staked literally thousands of killings on the basis of heresy against it. People were effectively executed by a catholic institution for providing a wrong answer to a question that the institution itself couldn't actually answer outside of more ambiguous language and contradictory concepts.
The Subtraction Problem
The problem with all of the shuffling of theology to accommodate an established orthodoxy is not just in the additions, but in the subtractions. There were key principles originally in the theologies that, as part of the inclusion of paganisms to resolve tensions, could no longer reconcile with the paganisms added. Thus, there were notable doctrines that were at first considered part of the orthodoxy which later became heretical as there wasn't enough room for them in the pew once Neoplatonism and Aristotelianism decided the pew was theirs.
Arguably the most empowering doctrine, deification, was removed on this very basis. Deification was actually taught by many bishops for five full centuries until it was decided to be a heresy - from Justin Martyr (100-165 AD) all the way through Maximus the Confessor (580-662 AD). Origen, Athanasius, and Augustine, founding fathers of catholicism, all taught this principle. Athanasius, who the third major trinitarian creed is named after (out of respect, not authorship), was actually quite clear in his view that the entire point of the incarnation of Christ was to pave the way for human deification - the same view LDS theology holds today.
As was with many other cases - catholicism eventually phased out deification because of the patchwork of philosophies it inherited. Omniscience, omnipotence, omnipresence, and absolute simplicity were all derived from Greece - that's not to say there isn't some biblical justification for them, at least the first three, but those notions were imported with their hellenistic lens into the pew, pushing deification out into the aisle. Thus, the removal of deification from orthodoxy ironically affords trinitarians the ability, in their framework of course, to label Latter-day Saints as heretics on the basis of agreement with over 500 years of Catholic bishops who created the foundation that Catholics and Protestants alike stand on.
The Salvation Problem
After the reformations that started in the 1500s, despite all of the divisions, one thing remained in nearly all sects - the trinity. Not every tradition agreed on every aspect of the trinity and some departed completely, but by lip service at least, most sects still claimed to be trinitarian. Even in attempts to reform and fix catholic orthodoxy, the prolific nature of Greek mysticism could not be defeated. As other essays have exposed, this agreement on the trinity proves somewhat meaningless as the question of how to obtain salvation is arguably far more pertinent to the individual than the exact metaphysics of the Godhead - especially considering Christ Himself spent His time telling us how to receive salvation and that did not include a lot of talk about what His mixture with the Godhead was like.
The trinitarian response to criticism of the focus on the Godhead typically revolves around the idea that you must know who to worship in order for that worship to be effective towards obtaining salvation. The problem with that notion is that the orthodoxy they insist on for knowing God expressly rejects the idea that God is knowable at all and insists on a performance of abstract language rather than a deobfuscation of that language. So we're supposed to know what God to look to for our salvation, while using contradictory, abstract, and confusing Greek language to achieve that knowledge. As the essay on the trinity points out, "Trinitarian theology on this question is so nuanced, so dependent on precise philosophical terminology, that to suggest it determines eternal outcomes is to argue that epistemological accomplishment saves."
The catholic theological framework that virtually all protestants share is built on the notion that God is essentially unknowable. Augustine, Aquinas, and others all made this express assertion, as a knowable God did not reconcile well with the pagan-sourced philosophies they were so heavily dependent on. So if we're supposed to point to the correct God while praying, but we effectively can't know to whom we're actually praying, how is obtaining salvation remotely possible? This is one of the most important contradictory circumstances the great apostasy produced and leads us to question how it is that we can verify we're performing the proper orthodoxy or anywhere near it.
Say you accept the trinity, in lieu of its tensions - how do you gain that salvation now that you're pointed at the correct Godhead? Here's where the trouble deepens - while there was some semblance of cohesion on how to talk about God, there is virtually none in how one obtains the salvation promised by that God. This, unfortunately, is by convention of any period of apostasy where man is left to try to figure out how to navigate on his own, absent a prophetic influence.
The Verification Problem
Augustine of Hippo (354-430 AD) and Thomas Aquinas (1225-1274 AD) both submitted that God is expressly unknowable and can effectively only be spoken of through analogy. This continues to be the philosophical view of all catholic traditions and only varied on slightly by some protestants. The problem with these two notions is that they logically make it a heresy to speak of God at all.
If God is unknowable, then it stands to reason that any language you use to identify Him cannot be more than a guess, with no way to know if that language is hitting the intended target. Using analogy to speak about God is an attempt at humility towards the unknowability, but it in no way resolves the problem of knowing whether or not the analogy you use is actually directed correctly. This is especially troubling for the charge of heresy that was lobbied against people for hundreds of years - how can you know that someone's committing heresy if you can't verify they've spoken incorrectly about God?
Some protestant denominations make an effort to rid themselves of this conundrum, but fail one step later. The protestant position that tries to resolve this tension states that God is somewhat knowable through scripture, just not exhaustively knowable. That's not an unreasonable position as it's arguable that you can't ever know anyone or anything exhaustively. The reason it doesn't resolve the tension is that the scriptures don't employ any of the Greek philosophical concepts or language employed in defining the trinity. This tension is then compounded by the fact that everyone seems to interpret the scriptures differently, especially among Protestants. To add insult to injury, Calvin's position was that God used accommodating language rather than exact language, such that our human minds could grasp what is possible for them to grasp. This means that even in Calvin's own explanation we're never achieving a knowledge of God, but rather some other thing we can understand. The explanation in support of the trinitarian's requirement of knowing God is almost a proof of the unknowability of God.
Conclusion
This document is not remotely exhaustive in its examinations of the tensions created by the great apostasy, it only serves to bring to light how fundamental and unresolved some of those tensions are. It serves to show that the issues of an Earth without a prophet are not small inconveniences, but untenable and catastrophic - leaving man in a state of confusion that he can't think himself out of. It leaves massive questions about the most fundamental parts of our salvation unanswered, surrounding the nature of God, the atonement, the resurrection, our fundamental duties, and our eternal outlook. The restoration of Christ's church doesn't just resolve tensions, it restores truths that were lost or mangled in the accumulation of texts and theologies. It restores coherence where there was little, and gives the saints a reliance on God Himself through revelation rather than their, or anyone else's, academic prowess.