When the news of this monumental disgrace reached the heart of the Imperium, the Inquisition, feeling itself subjected to an unparalleled insult, immediately arrested Grand Inquisitor Glapas and his subordinates, summarily executing them by white phosphorus cremation.
To be humiliated and released by xenos, to have an Industrial World destroyed for nothing while the aliens remained unscathed, the Inquisition could not tolerate such layers of infamy. Subsequently, the Inquisition and the Ecclesiarchy began to grant the Skaven some modicum of attention. This was motivated by nothing less than a burning desire to wash away their shame; failure to avenge such a public humiliation would cause both institutions to lose all standing.
Thus, the Inquisition and the Ecclesiarchy petitioned Roboute Guilliman, requesting that the eradication of the rat-men be placed under their sole jurisdiction.
Guilliman accepted this readily. In the eyes of the Lord Regent, these rat-men shared a relationship similar to that of Genestealers and the Tyranids. At this moment, the Regent was consumed by the monumental task of holding half the Imperium together and tracing the origin of the strange Warp powers backing these creatures.
Unlike his brother, the Lion, Guilliman did not overly concern himself with these xenos, whom he viewed as mere followers of a new Chaos power.
"I bear responsibility for this as well. I misplaced my trust in him. Glapas failed that trust, costing the Imperium untold resources and precious time," Guilliman remarked with cold indifference upon hearing of Glapas's execution. He had held a decent impression of the fanatically devout Grand Inquisitor, but such a catastrophic error demanded a price. Such was the iron law of the Imperium: Loss is acceptable; failure is unforgivable.
Massaging his temples, Guilliman sat upon his throne as Lord Regent and picked up a dossier, a summary of intelligence gathered from the Lion and Imperial agents regarding the rat-men. According to his calculations, though the Skaven were an unknown quantity, their threat level did not yet match that of other xenos or Abaddon. As Regent, he simply did not have the bandwidth to devote to a rising minor xenos species.
"Then I leave them to you," Guilliman said to the Inquisition representative.
"As you command, my Lord."
…
In the period that followed, the Inquisition and the Ecclesiarchy struck with full force. They organized thousands of clandestine investigation cells and Purge Squads, leveraging the Ecclesiarchy's massive secular influence to hunt for rumors of upright-walking rats.
What they found, however, terrified them.
Setting aside mere rumors, documented reports of Skaven presence within the Holy Sanctum of the Imperium covered nearly three-quarters of all Imperial worlds!
Agricultural Worlds were the worst hit, with their vast food reserves frequently vanishing. Forge Worlds and Mining Worlds were similarly infested. Immediately, the Inquisition and Ecclesiarchy shifted from rage to a desperate cover-up. Unwilling to broadcast their incompetence and dereliction of duty, they suppressed all news of the Skaven, declaring them to be nothing more than "vile mutants" transformed from underhive dregs.
They could never admit that, through their own negligence, the Emperor's holy domain had been shared with these foul xenos for an unknown length of time.
They subsequently deployed tens of thousands of rat-hunting parties to various worlds. Most of these operations, however, were merely repetitions of the disaster at Trier. Fanatical Inquisitors either searched aimlessly through the labyrinthine machinery of Industrial Worlds, stood watch over granaries for years on end, or vanished forever into the bottomless pits of Mining Worlds.
These locations were undoubtedly the most perilous. Some Inquisitorial teams even stumbled upon Skaven infighting of a staggering scale.
On a Forge World known as Kato XV, the local Skaven had long been conquered and assimilated by Claw-Warlords of Clan Verminus dispatched from Holy Terra. Bolstered by the world's vast output of weaponry and industrial goods, the Skaven population there had grown exponentially.
When an Inquisitorial hunting party descended into the mine shafts, they were wiped out by an overwhelming tide of rat-men. These vermin were fully armed; many even had portions of their bodies replaced with mechanical augments, mimicking the Adeptus Mechanicus. As a trophy of war, the leading Inquisitor was taken prisoner and cast into a filthy, lightless cage.
In that stench-ridden hole, he survived only by praying to the Emperor, until the day the local Skaven suddenly became hyper-reactive, as if seized by a collective terror.
"The Emperor protects... your end is near, xenos! Once the Imperial host arrives, you will have nowhere to hide!" the filthy, skeletal Inquisitor croaked. He was barely recognizable as human, yet his curse remained firm.
The Skaven ignored him. Using a rusted chain, they kicked and beat him, dragging him out like a dog. Upon emerging, the Inquisitor realized it was not an Imperial host that had arrived, but another army of rat-men.
These newcomers bore different banners. Most wore complete suits of armor resembling Power Armor and donned gas-mask apparatuses. Their weaponry was entirely alien to the local breed. Looking at the path they had carved, it seemed the entire Forge World had been seized by these newcomers.
The Inquisitor's suspicion was correct.
In just a few months, a Skryre Hive Fleet, having translated through the Warp, had engulfed this world, which had already been weakened by Clan Verminus's harassment, using an overwhelming rat-tide and terrifying Warp-weaponry. Once Ikit Claw reduced the local Archmagos to boiling slag with his Warp-fire, the Skryre legions began systematically seizing the planet.
Naturally, they pushed into the subterranean depths, intending to press-gang the "primitive" local rats who hadn't even formed a proper clan.
Clan Verminus was stunned. Within the Holy Sanctum of the Imperium, they had grown accustomed to "looting an empty supermarket." This was their first time facing an assault from their own kind. The meeting of Clan Verminus and Clan Skryre was like Neanderthals encountering Homo Sapiens; both sides were momentarily paralyzed by the sight of the other.
Then, a Clan Verminus Claw-Warlord, half his body augmented and clad in heavy ceramite Power Armor, wielding a long-handled Power Sword and a Warp-bolter, stood atop a modified "Leman Rat" tank. From a safe, arrogant distance, he shrieked:
"What-what are you? What things?! This is Clan Verminus territory, YES-YES! The claws of Supreme Klaw-Marshal Whitesick, Chosen of the Great Horned Rat, protect these warrens!"
Ikit Claw tilted his head, listening to this rat-man shouting a completely foreign name under an unknown banner. Within his brilliant, mad brain, there was no record of a "Clan Verminus" or a "Supreme Klaw-Marshal Whitesick."
"Have these slaves already entered the tribal era? That is... inconvenient."
Ikit's lightning claw clicked and snapped open. Beside him, a Warp-Warlock driving a Flayer shouted back:
"Your pathetic-trash clan is finished! Become part of the strong-great Skryre, you wretched slaves! Or else, taste-feel the might-power of Skryre!!"
One side was the most expansive power within the Imperium's borders, the other the strongest force in the Imperium Nihilus. Neither would yield. In the true fashion of the Skaven, they chose the only way to settle the dispute: they opened fire.
Thus, the two terrifying rat-armies, the modified Imperial tech of Clan Verminus and the Warp-science of Clan Skryre, erupted into a chaotic, bloody civil war.