Age of Redemption
Basically, the Imperium, fresh off the Thorian Reformation, decided to expend all of its troops in penitent and redemptive crusades instead of, you know, actually defending its borders. This would prove to be a bad idea... at least, if you listen to the core rulebook. You see, the writers seemed to have goofed. The Adepta Sororitas fluff states these were Wars of Faith, which are called by the Ecclesiarch and only include the Adepta Sororitas and whoever else wants to join them (i.e., it's not exactly mandatory). Theoretically, this means that the Imperium should be better off than it was pre-Apostasy (Sisters burn xenos, don't burn loyal citizens), but apparently this isn't true.
Sometimes mentioned in fluff relating to the Adeptus Mechanicus, the Occlusiad was a time period when a radical sect of Tech-Priests, calling themselves the Apostles of the Blind King (probably no relation to the Silent King), declare humanity to be an affront to the Machine God. Then, for good measure, they uncover a bunch of archeotech that lets them blow up stars. This actually is more likely than it seems. Considering how often the Adeptus Mechanicus priests/generally everyone go insane, it's not so unlikely one of these rogue sects manages to get their hands on world ending technology. Probably a lesson to be learned here somewhere.
War between the Imperium and the Apostles rages for a decade until a Navigator by the name of Joyre Macran accidentally discovers the palace-warship of the Blind King in the Warp. He brings an Emperor-class battleship called the Dominus Astra and blows up the Blind King. Without their leader, the cult is finally ended.
One of the more important events of the Age of Redemption was the Abyssal Crusade. Basically, a Chaos-worshipping Ecclesiarch (apparently such things exist) sent thirty Chapters of Space Marines on a crusade into the Eye of Terror, where most of them went renegade.
A bunch of optimists, mostly children, decided they could change the galaxy for the better with love and tolerance. They decided to go on a pilgrimage for Terra, calling themselves the Children's Crusade.
They reappeared almost a thousand years later, most of the ships twisted and torn beyond recognition. It was renamed the Lost Crusade, and the Inquisition tried their hardest to cover it up. It's almost as though blind optimism and hope attracts negative warp entities.
Also, for some reason, the BRB gives the title "Dissidence Dreams" to the whole event, but it's not clear why.