Much of this (or at least a sanitised version of it) was public knowledge in character. There were of course other things going on during these periods, they just weren't plot relevant.
God created the universe. Following its fixed mathematical laws, it had no tendency towards good or evil (as God saw these concepts), thereby allowing its creation despite the restriction on God's power, but it held the potential to be guided towards good.
Next, they created Heaven, Hell, angels, and demons, with the angels being the ones meant to be guiding the world towards good, and the demons existing as a side-effect. The plan was that angels would be able to cooperate with each other and demons would not, so the angels would tend to have more influence, which mostly worked except that promoting chaos is often simpler and easier than promoting order.
For a very long time, Heaven and Hell watched for anything interesting to develop. They had their own things going on internally, but their influence on the physical plane was always the main point. Eventually, life and then humans arose.
With a more worthwhile target, the angels and demons started interacting more with the world, both trying to guide humanity in their direction. With society mostly very fragmented in small tribes, a limited number of angels and demons available, and no better way of transmitting teachings than oral tradition, there was not all that much that either could do. Some societies were influenced by demons, developing traditions of risk-taking, violence and mistrust, and some were influenced by angels, towards caution and cooperation. Some had neither, and developed on their own. Very few people were beatified, because Heaven considered it too uncertain how someone who had such a limited amount of information about Heaven while alive would act later.
In the bronze-age kingdom of Palesheh1), writing developed for the first time, giving an opportunity to spread Heaven's influence more broadly with less direct interaction. Tabaga gave the first scripture, which was shortly followed by many more revelations explaining the basics of how Heaven wanted people to live, and explaining more about Heaven itself.
Having firmly established their influence on Palesheh, Heaven gradually expanded it along with the spread of literacy. The scripture continued to be expanded, though more slowly than before, with Heaven cautiously taking time to check how changes to their advice were taken now that all the basics had already been established. By 700, almost all of the world was at least somewhat connected and around half of the societies at the time were literate and under Heaven's influence, but some of the remainder still openly followed demons.
With their influence nearing reaching the whole world, Heaven started pushing more towards completing it. They took more of an active role in human politics, and gave some more revelations about spreading the word. This worked, in that their influence did spread more, but also went terribly, in a series of events later known as the Holy Wars. The tech level at the time was early iron-age (in some places at least).
Seeing all the war it had been causing, Heaven tried to take back some of the earlier statements that many humans had taken as a mandate to conquer the infidels (while also avoiding losing face too much), but the humans were having too much fun with all the conquering and didn't pay attention to what they didn't want to hear. This led to one of the very few revelations directly from God, in June 905: “Wage no wars and fight no battles in My name. No matter who your enemy is, all mankind are My people.”. Like God's final revelation, this was delivered simultaneously to every person on Earth. A combination of this, all the previous anti-war revelations from angels and saints, and running out of infidels to conquer eventually led to an end of the Holy Wars. From this point, Heaven became much more reluctant to interfere directly in human politics.
With everything vaguely under Heaven's control, things calmed down somewhat. The high level of caution Heaven imposed led to steady but slow scientific and technological progress, with each new breakthrough having to be thoroughly examined before it could be implemented. Around 3500, the industrial revolution started and the pace of progress picked up somewhat but remained cautious and slower than happened in real life.
Some demons came close to completing a plot similar to the one Slzlth, Thrl and Pfmsltr were doing in 3914, with the goal of killing God. Heaven had always known this was a theoretical possibility (intentionally so), but until this point had not realised how much of a risk there actually was.
In order to prevent a repeat of the demonic plot, Heaven suddenly started taking a much harsher stance on demons and witchcraft. Many new anti-demon revelations were given, and Heaven pushed for the creation of the Commission. Technically the Commission already existed, but up until this point it had been a much smaller organisation mostly dealing with collecting and distributing scripture. With the new mandate from Heaven, and a continuous stream of information from God to help them complete their mission, the Commission grew dramatically in power, taking over much of the authority that had previously been in the hands of many smaller nations, and becoming the organisation is was at the start of the game.
Meanwhile, Slzlth worked in secret to bring an updated version of the plot to completion, culminating in the events of the game.