Just today, I got a really weird idea for a Warhammer 40k/MLP:FiM Crossover vaguely similar to Ciaphas Cain, Warmaster Of Chaos. I'll post the summary I typed up here:

So... my name is Ciaphas Cain, and I am—or, at least, I was—a newly-minted Commissar fresh out of the Schola Progenium. By some horrid twist of fate, I got assigned to the Valhallan 18th and its infamous Commander, which has just been sent to a newly discovered backwater garden world to dispose of its oddly horse-like xeno population. 

The next thing I know, I'm stranded on the planet in an alien body, the Xenos’ leader is in a coma for the foreseeable future, and her subjects—despite knowing full well that I was once a member of the same group of Imperials who’d struck her down—have shoved me onto her now-vacant throne for reasons having to do with the fact that my new body has wings and a horn. And I'm apparently a psyker now thanks to that horn, and a stupidly powerful one at that. Oh, and have I mentioned that these xenos expect me to somehow lead them to victory against the trigger-happy Inquisitor that seeks to wipe them off the face of the galaxy with nothing but my savviness, a cunning mind, a silver tongue, the resources of a race completely oblivious to the grim darkness of the far future, a 'care package' consisting of an STC database of everything a Imperial Guard regiment could ever needed from a "spirit of chaos" that is responsible for my current predicament and may or may not be Malice the 5th chaos god, and the magical power of peace, joy, rainbows, and orbital friendship lasers? I don't think I had.

Brace yourselves; things somehow manage to get even wackier from there. 

Questions, thoughts, concerns? Feel free to leave a comment.

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SOLD!!

I actually had a similar idea. Only mine had Cain's regiment stranded, Cain has to keep his Guardsmen from starting war with the mostly Psyker Xenos that they are not prepared to fight (no ships/air support or titans), Applejack immediately hates his guts cause she can sense he's a fraud, and the main villain is Sombra who uses his power over fear to expose Cain to his regiment.

God, I wish I had time to pursue this, but I already have four incomplete fics I need to finish first.

Go for it as long as it reads similar to warmaster of chaos or the original ciaphas cain series it is guaranteed to be wildly popular. You might even be able to consult the author of warmaster of chaos for ideas if you get writers block.

7944982
I would like to read that.

I would like to see Cain's men kinda have known all the time, or at least most of it, but still followed him because they knew he actually cared what happened to them.

Or you could do a classic: kills sombra and rules the crystal empire before the princess of love whose name I can't remember how to spell gets there and is unable to just give up the throne because the people refuse to be ruled by anyone other than CIAPHAS CAIN SAVIOR/EMPEROR OF THE CRYSTAL EMPIRE worshiped by his people

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I’ve gone for it.