Age of Apostasy
The Age of Apostasy is one of the major time periods of the Imperium of Man. It was preceded by the Nova Terra Interregnum and followed by the Age of Redemption, stretching from the beginning of M36 to 010.M37. It's basically the Protestant Reformation IN SPESS.
Wars of Faith
Contrary to popular belief, the Age of Apostasy actually started much earlier than the Reign of Blood, and had its roots in M33 with the establishment of the Temple of the Saviour Emperor, which was basically the Vatican 40k-style, and its position amongst the High Lords of Terra allowed it to actually impose taxes on the citizens of the Imperium.
There had been many separate cults of the Emperor, but the Temple either swallowed them all up or obliterated them, to the point that the only cult that challenged them was the Confederation of Light, a more penitent cult that was all about "giving" in the name of the Emprah, rather than building up big cathedrals and palaces. Eventually there was a big war and the Confederation was removed as a major power player.
The Temple of the Saviour Emperor would only grow in strength as they accumulated wealth (via taxation that should rightly have gone into the government funding) and power since they had a religious army to back themselves up, eventually causing the Administratum to wane in power to almost pointlessness - which is funny because no government would ever let someone else take its power or its money. The moment they started taxing, any government would have shut them down (perhaps literally), with any complaint met with "I'm sorry, I can't hear you over the sound of my soldiers killing you for sedition." This is especially funny when said government can easily argue that it was approved by the Emperor personally while he was still walking around whereas the religious organization merely claims that the Emperor approves of them despite forming long after he was put on the Golden Throne. Hell, the Administratum is even considered a kind of priesthood by the common folk, so technically the Administratum is the "true" Imperial Cult and could easily use that in its arguments to nip rebellion in the bud for when the Administratum sics the Hammer of the Emperor upon the morons trying to steal its money.
There was a period of clever politicking when the Administratum thought they were on the comeback, but then the Ecclesiarchy declared "Screw you guys" and moved the seat of their power to Ophelia VII in a very expensive undertaking where they built new palaces for themselves and left Terra to rot. The only reason this would have mattered is because of the taxation thing, otherwise it only would have cost the Ecclesiarchy its own money gained through optional donations (required donations being considered taxation if the money-sniffers have anything to say about it). 300 years later, the Ecclesiarchy figured enough time had passed that they were in no danger of being messed with and returned to Terra, raising taxes even further to fund the move.
Funnily enough, this particular clusterfuck was based on a real period in history where the Holy See was moved from Rome to Avignon and back again during the 1300s due to the French king's influence over the Catholic Church, which had the same general effect on Rome as it did on Terra due to how closely interwoven the Church was with Rome. However, unlike the real-life Church, the Ecclesiarchy grew loooong after the government it co-existed, meaning nothing like this was actually possible, especially letting them have a full-fledged army of their own. But, hey, you gotta suspend your disbelief in 40K. Sometimes so high that it requires blind faith.
The Reign of Blood
The main event in the Age of Apostasy began around M36, when Goge Vandire, Master of the Administratum, had the Ecclesiarch assassinated and took control of the church himself. 40K being 40K, power went to his head and he began the so-called Reign of Blood in which he purged the Imperium of any dissenters with the backing of armies of millions of frenzied Imperial Cultists and a personal army called the Frateris Templars.
Eventually, the people of the Imperium grew tired of Vandire's rule, and when a young man named Sebastian Thor started warring against the mad High Lord he was soon joined by a massive army known as the resurgent Confederation of Light (since the original followers had just gone into hiding). Vandire sent a fleet to deal with Thor's army, but when it was destroyed by a massive Warp Storm that appeared out of nowhere (and is still there by M41, called Storm of Emperor's Wrath), people took that as a sign that the Emperor favored Thor and he became even more popular.
When Thor finally got to Terra, he joined forces with the Space Marines and Adeptus Mechanicus (who had never been friendly with the Ecclesiarchy to begin with) and managed to dislodge Vandire, forcing him to retreat to the heavily-fortified Ecclesiarchical sanctum of the Imperial Palace. With a Space Marine force spearheaded by the Imperial Fists and their successors it was assumed that Vandire would be easily overwhelmed. You can imagine the Coalition's surprise when instead of zealous but ineffective Frateris Militia they unexpectedly were faced with a force of superbly trained and equipped warrior-women clad in Power armour, wielding Bolters, skilled enough in warfare to challenge even Space Marines and holding their ground to the last woman in their utter, complete and absolute conviction they were defending the Big Guy himself. This was The Daughters of the Emperor (temporarily renamed "Brides of the Emperor" because Vandire was implied to be maybe probably definitely absolutely using them as sex slaves), and they proved to be too well entrenched for the Astartes' premier fortification-breaking experts to overcome quickly; what should have been a beheading alpha strike bogged down to the point it looked like it would turn into a massive meat grinder. Luckily for everyone involved, Thor had a Plan B: the Captain-General of the Adeptus Custodes managed to infiltrate the compound (he and his warriors had remained at their post defending the Emperor at the centre of the Palace without intervention so far, or so Vandire thought) and brought Alicia Dominica, the leader of the Brides/Daughters of the Emperor, to a face-to-face meeting with Big E himself. What exactly was said between the Emperor and the woman who would become the first leader of the Adepta Sororitas is unknown, but it's really not hard to guess that the essence of the message was 'My Daughter, Vandire deceived you and serves only himself'. When Alicia Dominica came out of the throne room, she was filled with such Rage that she ended up personally executing Vandire herself. His last words were "I don't have time to die; I'm too busy".
With Vandire dead, Thor became the new Ecclesiarch (initially refusing the position, but the Adeptus Custodes commanded him to either take the position or die) and he instituted some reforms. First, he toned down the Ecclesiarchy's grandeur, insisting that the Church serve the Imperium as much as the other way around. Second, he issued the Decree passive, a law which stated that the Ecclesiarchy should have no "men under arms". Finally, since he realized that the Ecclesiarchy still needed an armed force in case another Vandire tried to spring up, he reformed the Daughters of the Emperor into the Orders Militant of a new, all-female branch of the Ecclesiarchy, the Adepta Sororitas, reasoning that the Decree Passive didn't forbid them since they were women under arms and that the Ecclesiarchy shouldn't be left totally dependent on the other parts of the Imperium for its defense. Even in the grim, dark future, there are still rules lawyers.
If you're still trying to untangle the issue, remember that most of Vandire's former victims wanted the Ecclesiarchy up and gone. Hearing that Thor's second and third reforms were seemingly mutually exclusive probably shut them up with happy smiles, and hearing that the pious and largely-incorruptible Daughters would be doing the policing likely didn't raise any further complaints (and those that did complain shut themselves up quickly).
MERCIFULLY, this infamous case of semantics fuckery was actually resolved in pretty badass fashion by the 8th Edition version of Codex: Adepta Sororitas in 2019. Witnessing the furiously fiery faith of the Daughters of the Emperor and recognizing the need for the missionaries and standing churches of the Imperial Cult to have a way to defend themselves, Sebastian Thor went to bat for the Daughters. Thanks to the momentum of, you know, saving mankind from a raving lunatic with delusions of grandeur, he was able to strongarm the High Lords into exempting the Daughters from the Decree Passive and allowing them to reorganize as the Adepta Sororitas we know and love today, with the caveat that the Sororitas have the responsibility of basically being the Ecclesiarchy's version of Commissars. Awesome guy, that Sebastian Thor. So on the one hand, the Ministorum is happy to have the nuns with guns under their authority; on the other hand, the nuns with guns constantly watch the Ministorum and its personnel for any sign of corruption be it Chaotic or mundane and don't hesitate to get their flame on at the first hint. This hasn't stopped them from putting the Ecclesiarchy's desires first on occasion, though (which considering the Reign of Blood should have immediately gotten the offenders purged).
Finally, the Moirae Schism of the Adeptus Mechanicus (which had been ongoing since the Nova Terra Interregnum) was peacefully brought to an end with Thorian reformation and the schismatics were allowed to rejoin the Orthodox Tech Priests, while the Sons of Medusa Chapter made up of Iron Hands and Marines from successors believing in the Moirae doctrine (minus the Red Talons who killed all of their schismatics) were judged to be pure and their unofficial founding was formally ratified by an edict by the restored High Lords, finally bringing an end to the last major problem of the Nova Terra Interregnum as well.
To make sure these new reforms were followed, the Inquisition set up the Ordo Hereticus to both police the Ecclesiarchy and protect the purity of its teachings, with the Battle-Sisters serving as the Ordo's Chamber Militant.
It's still pretty darn weird that the Brides of the Emperor weren't brutally purged by the furious mops of everyone-in-the-galaxy, though. Having a last=second change of heart doesn't make you innocent of the horrors you committed or willfully and knowingly enabled. Realistically the moment the Sisters stepped outside of the Palace they would have been blasted to hell by furious soldiers and citizens.
As proof that no good deed goes unpunished, Thor's head got taken by Trazyn the Infinite, making Trazyn no less than the fifth person to have claimed that valuable skull. No kidding, the paperwork is such a clusterfuck that three different Sororitas shrines and at least one Chaos jackass all claim they've got Thor's skull knocking around in their attic somewhere (although to Trazyn's credit, this head is preserved in a jar, which makes it more plausible he did get the original).
Plague of Unbelief
Another minor event was the Plague of Unbelief in which a rogue Cardinal built a personal empire after Terra was cut off by warpstorms towards the end of the Reign of Blood. The idiot might even have gotten away with it too, but then he got the genius idea to bother the Space Wolves. With his armies in shambles after learning the hard way that you shouldn't rouse a sleeping Wolf, it gave Confessor Dolan Chirosius the opportunity to start a revolt that would ultimately give the crazy dumbass the boot.
On a galactic scale it's not a particularly important event, but as a story it is full of Awesome.