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Assume that the X-men pop up in the IoM, can they take on the emporer?

No way. The emperor is the most powerful human EVER!!!

He has billions of billions of billions of subjects.

He ROCKS!!

The space marines, inquisition and adeptus custodes would annihilate the x-men before they could get anywhere near the emperor.

do any of you know were to find the graphic novels on this series? as in all of them.

THere are various comics for 40k. There was 'inferno' and 'warhammer monthly'
and there is the Bloodquest TPB

The Imperium of Man has been honed over many, many thousands of years to destroy three things. 1. Heretics. 2. Aliens. 3. Mutants. Somehow I think the X-Men would be quickly taken out without ever inflicting much damage on, or even coming close to the Emperor.

And any good "Games Workshop" should stock any and all Warhammer types stuff (like the graphic novels, comics etc)

They have an entire galactic infrastructure designed to eradicate mutants from the galaxy, even if it means killing millions of innocent lives and blowing up loads of planets to do so.
The x-men would be killed straight away