Age of Apostasy
The Age of Apostasy is one of the major time periods of the Imperium of Man. It was preceded by Nova Terra Interregnum and followed by the Age of Redemption, stretching from the beginning of M36 to mid-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 with its position amongst the High Lords of Terra would 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 which was a more penitent cult that was all about "giving" in the name of the Emprah, rather than building up big cathedrals and palaces.
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.
There was a period of clever politicking when the Administratum thought they were on the come-back, 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.
300 years later, the Ecclesiarchy figured enough time had passed and they were in no danger of being messed with any more, and returned to Terra, having to raise 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.
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. Vandire proved difficult to unseat, as he was protected by an order of warrior women once known as the Daughters of the Emperor (renamed the Brides of the Emperor when he convinced them to serve him).
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 (the Black Templars, the Soul Drinkers, and several others) 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 who held their ground to the last woman in their utter, complete and absolute conviction they were defending the Big Guy himself. The Daughters proved to be too well entrenched for the Astartes premier fortification breaking experts to overcome quickly and 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, 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) and brought Alicia Dominica, the leader of the Brides 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 renamed her sect the Daughters and 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. Bad ones, too, since any fool could point out that "men" also shares the definition of being another name for "human", thereby making any church Chamber Militant, regardless of gender, illegal. Of course, it is heresy to point this out, and heresy is decided by... oh. On the bright side, imagine how the Sororitas and the rest of the Imperium would react. The former is so fanatical they might genuinely kill themselves for being a "sinful existence" or some such. The latter would probably launch another reformation crusade in fear of a second Reign of Blood. After killing the "heretic" who pointed out the discrepancy. After all, if the Ecclesiarchy refuses to acknowledge that "men" also means "human" then they would be officially declaring half the species to no longer be considered human. The Imperium would not react well to that. To put it mildly, the Ecclesiarchy may well not manage to survive as an organization after the fallout from that.
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).
Anyway, 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.
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. I wish I was 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.
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 that you shouldn't rouse a sleeping Wolf the hard way, it gave Confessor Dolan Chirosius the occasion 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.