Age of Apostasy
The Age of Apostasy is one of the major time periods of the Imperium of Man. It 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, led by his Preachers. Vandire proved difficult to unseat, as he was protected by an order of warrior women known he co-opted known as the Daughters of the Emperor, which he renamed "Brides of the Emperor".
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 Coalition of Light. Vandire sent a fleet to deal with Thor's army, but when it was lost in the Warp, 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 the Daughters proved to be too well entrenched for the Astartes premier fortification breaking experts to overcome. The Adeptus Custodes managed to infiltrate the compound (as they defended the Emperor, who was at the center of the Palace) and brought Alicia Dominica, the leader of the Brides of the Emperor, to a face-to-face meeting with the big man himself. What exactly was said is unknown, but 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, and he instituted some reforms. First, he toned down the 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, he reformed the Daughters of the Emperor into the Orders Militant of a new, all female branch of the Ecclesiarchy, the Adepta Sororitas (as they were women under arms) to serve as the Church's armed force.
As proof that no good deed goes unpunished, his head got taken by Trazyn the Infinite.