Another one, because I think the vilification of Nurgle isn't completely fair. Same disclaimers here, I don't know jack about WH40K canon:
The Stoics
The Imperium was ignorant of the fact, as it usually is, but the Protectorate's infamy among worshippers of the True Gods (who still held themselves to their gods in their true form) was greater than that of her infamy in the Empire. Whoever had heard of a man who embraced Three of the Four, and accepted those who still worshipped the Anathema? And worse, turned the vitriol of the rest of the Three's worshippers from the Corpse King to the Grandfather? No no no, the Great Unclean ones chortled, Warmaster Cain's reckoning will come one day, and Grandfather will regain his rightful place at the head of the table of the True Four, without the sacrilegious influences of the True Heretics of Slawkenburg. (Some reformed Neverborn were overheard chuckling about some likely-xeno race called "Scotsmen")
And it seems like today, seven hundred years after the Liberation, the Grandfather would have his due.
After multiple centuries and countless barely-repelled Black Crusades, Roboute Guilliman had finally managed to wrangle the Administratum into a halfway decent form, and centralized enough power to properly scrutinize the Protectorate. It had expanded to almost a tenth of the size of the Imperium itself (Cain had long lost hope of containing the Liberation Council, and accepted that they would be the Imperium's serious rivals), and had gained a reputation for consistently winning at hundreds-to-one odds against both Imperial and Heretic forces during the Crusades. Guilliman did not forget its fighting prowess, nor the fact that they avoided Imperial forces whenever possible and usually aided them, and extended ambassadors toward the Protectorate. A stable alliance was achieved, Panacea became even more widespread, and it appeared that finally, in the grim darkness of the 42nd millennium, there was peace. There were even rumors that the Panacea was slowly healing the God-Emperor himself.
But as the God of Entropy is so fond of reminding others, nothing, especially nothing good, ever lasts.
The citizens of the protectorate, especially on Slawkenburg, Adumbria, and Cassandron had been a blissfully happy bunch. They all remembered clearly the corruption and evil of their oppressors, be they Imperial or Nurglite. The sweeping reforms made by the Liberator turned intolerable hellscapes into unimaginable paradises, and in their uplifting, the worship of both the Reformed Gods and the Emperor flourished. Khornates saw their liberation as justice getting its due, Slaaneshis saw their increased, sustainable pleasures as a sign of the Prince's approval, Tzeenchians viewed the new era of knowledge and curiosity as a blessing from the Architect, and the worshippers of the Imperial Creed were swayed by Cainite Reforms into believing the Emperor had overcome the dupes of Nurgle to return to blessing Mankind once more.
The passing of the Liberator was mourned, but even so, the Protectorate was in her golden age. Even with the constant use of Panacea, The Liberator was still mortal, and one morning, his bed was found empty, with nothing but a mark of Slaanesh on it. The Handmaidens immediately discovered his Ascension (but did not disclose that he was some never-before-seen hybrid of Imperial Saint and thrice-blessed Daemon) and joined his beloved Emeli's side. Around the same time, the original generation of the Liberation Council started succumbing to the ravages of age as well, with only Malicia and Zerayah left from the original group of heretics who rebelled against their oppressors.
No matter, for the equally beloved Zerayah Cain took over her father's reign. Her rule was just as wise and blissful as the Liberator's, seeing them through peace, through a Nurglite plague that devastated their crops, a Necron awakening that they required the Imperium and the Tau's assistance to put down for good, and more uncounted crises that would exterminate the Protectorate were it under the aegis of an inferior leader.
One day, though, Zerayah Cain disappeared. It was the latest war, one final one against the Tyranids, which required an alliance of all civilized races in the galaxy; the Protectorate, the Imperium, the Tau, the Eldar, and even the Orks, who were somehow able to be convinced that if the bugs don't die, there would never be any more krumpin' ever again. It was the final campaign; the last bioship, still running rouge in the unknown reaches of the galaxy. There were shield worlds and Annihilator-Class planet-ships at the other edges of the universe, ready to repel any new incursions. With the destruction of this final bioship, the Tyranids would be dangers no longer. Zerayah Cain was even more famous than her father for leading at the front lines, and at the penultimate battle, Zerayah led the final flight of Cainwings toward the bioship to cripple all of its remaining guns before battleships could destroy it. The mission was an overwhelming success, with only two casualties.
Malicia. And Zerayah.
The Protectorate was absolutely devastated. Against almost all advice, the USN commanders insisted on a board and search to destroy the ship and find Zerayah, which nearly brought the the formerly ironclad alliance to war. Finally, the other nations, save the Orks, agreed, on the condition that the Protectorate had no support. They were not willing to risk their own for such a suicidal mission. The Protectorate readily agreed and turned an overwhelming success into an unmitigated tragedy.
The bioship was happy to consume parts of itself to produce new soldiers to combat the USA, USSM [space marine], and Ork troops that landed on it, causing casualties that made even the oldest Imperial Guard commanders blanch. No matter how excellent their training and augmentations, even an Astartes was no match for the Tyranids inside their infernal bioships. Wave after wave of troops were landed onto the ship, and wave after wave died unspeakably horrific deaths, their biomatter consumed to make more Tyranids for their comrades to kill. The military force known to consistently inflict a million-to-one casualty ratio could barely keep a 1:1 in the bioship, many troopers dying before even firing a shot in their desperation to find Zerayah, while the Orks had the time of their lives. The entire task force was nearly depleted before the Imperial Commander took pity on them, intercepted the last of the troop transports, and blew the bioship to oblivion.
Despite the enormous casualties, troopers had reached every corner of the bioship in their search with their helmet cams on. Nothing. The space around was searched. Nothing. The nearby planets, subsectors, Segmentum. Nothing. Zerayah was gone.
Unlike the Liberator's passing, which was still greatly mourned, the citizens of the Protectorate were despondent. The pain of Ciaphas' passing could be tempered by the certainty that his daughter was just as great and ready to take over his duties, but who could live up to the glory of House Cain? Nobody, not even the most egotistical members of the Liberation Council thought they could do so. It was thus decided that the heads of the cults should form their own government, with a representative from the USM [military], the Handmaidens, the Tzeenchians, the Eclessiarchy, and the Borgs forming a council to rule the Protectorate.
However, no matter how wise their decisions were, everyone agreed, including the council themselves, that they were inferior imitations of greatness. Truly, the Liberators could not be replaced. Justice started to feel ridiculous, for what mockery of a just universe would allow a brilliant soul like Zerayah to pass so viciously? Passion felt meaningless: what was the point of overloading your senses when you know your loved ones will never come back? What is subterfuge without a worthy cause to trick for? Technology without a cause to serve?
For the first time in more than seven hundred years, the loving arms of the Grandfather drifted around Protectorate hearts to comfort those poor, desperate souls.
Well this ballooned out of my control. I'll finish it later.
Killing off Ciaphas and disappearing Zerayah are the only ways I can think of to make the Protectorate not a literal paradise, which is necessary for my story to work. It won't be grimdark, but I want it to be somewhat realistic.