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I have had an Idea for an IG army that is both part of the IoM and not. So, it has been recruiting slaves(mutants) and has been declared heretical by most, but still fights for the emperor. This is an Idea that some may take for themselves because I have no plans on using it.

Interesting, I feel like the imperium may use them for suicide missions and then if that doesn't work would cast them out as heretics.

They'd probably be declared heretical immediately, that seems to be how things work in the Imperium. But then there's a Blood Angels successor chapter who were declared heretical yet still fight for the imperium I believe..?

There's a wide spectrum of human forces in the service of the Imperium. The fluff is replete with Inquisitors at odds and IG regiments fighting one another. I don't think it's ever so clear as "these guys are heretics, go kill them." Even in actual human history there are plenty of times that a society would overlook such issues if the situation calls for it. A regiment that might be traitorous in the eyes of one Inquisitor might be glorious in the eyes of another.

I like the idea of a force of underhive mutants enthralled by the Imperial doctrine, searching for redemption in the eyes of the Emperor. Perhaps an Inquisitor sees that they'd be useful troops for fighting in hazardous environments that would kill most normal humans, and he figures "let them die fighting for the Emperor. It'd be traitorous to destroy such an asset."

My own army's fluff is that they're an agricultural world recently integrated into the Imperium, on the edge of Tau space and with a high incidence of psykers ("chosen"). The Imperium is slowly reshaping the political atmosphere on the planet, driving out the influence from years of trade with the Tau, and Imperial priests are converting the population from their solar-worship into the Imperial creed.

The Imperium may be a crazy place, but they're not insane. Imperial agents aren't necessarily going to destroy a force that is eager to fight for them when they could gain that force and let it destroy itself against the Imperium's enemies.

Put an inquisitor in charge of the army and it is fluff kosher. Inquisitors have so much carte blanche they can field demonically possessed squads, I am sure a few mutants won't even register.

BTW ogryn and ratlings are both types of true breeding mutant strains. So your idea is not so far out there.