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This idea has been driving me nuts for the past week. Skaven are just a cool race, and how could they not be in 40K? So i was thinking, why not create a guard or ork army using Skaven models and converting here and there? Looks like it could be done easily enough with las pistols for sluggas or some such. Could just say they were souped up laspistols. Any other ideas?

Yeah, I'd say mutants in the service of the Imperial Guard might be your best bet.

Another idea is Chaos. You could make mutated Chaos Marines, or pray for a return of Lost and the Damned and make mutant cultists.

isnt there already a skaven race that has some sort of entropic effect associated with them. The Hrud or something.

http://www.google.com/imgres?imgurl=http://images.dakkadakka.com/gallery/2010/9/26/142500_md-Clanger,%2520Conversion,%2520Greenstuff,%2520Hrud,%2520Painting,%2520Rat,%2520Skaven,%2520Warhammer%252040,000.JPG&imgrefurl=http://www.dakkadakka.com/gallery/142500-.html%3Fm%3D2&usg=__qkdZgi89XB3SA4xMfnA07Gj4Y2c=&h=600&w=800&sz=30&hl=en&start=20&zoom=1&tbnid=9QwcrnN6LYq2UM:&tbnh=107&tbnw=143&ei=N-8LTqCaIIi4sQOgzOGYDg&prev=/images%3Fq%3Dhrud%26hl%3Den%26sa%3DX%26tbm%3Disch&itbs=1

http://warhammer40k.wikia.com/wiki/Hrud

Yes, but whose to say Skaven can't exist in 40k? Some dimensional rift or some such brings over a large group of skaven, and after a couple hundread years they develop and become horribly numerous across dozens of worlds.

EDIT: Wow, so THATS what hrud are? Always wondered. I apologize for this post, i was probably in the middle of posting it as you guys posted your own, but still, i like the original idea for the hrud.

If you do a search in the P&M Blogs, you should be able to come up with a number of threads on Space Skaven. I know that Blackhand has one (his gallery is here: http://www.dakkadakka.com/gallery/images-19931-9734_Blackhand%27s%2040k%20Skaven.html, but I can't find his P&M blog at the moment.) Joshoftheforest's Space Skaven (Nezumi) blog is here: http://www.dakkadakka.com/dakkaforum/posts/list/329280.page and I'm pretty sure that there are links in there to Blackhand and Santobell's Space Skaven blogs - there's also a discussion about how Hrud =/= Space Skaven on page 3 or 4 or so.

Finally, outside the Dakkaverse, there is Nyhil's Space Skaven at his blog Ten Inch Template here: http://teninchtemplate.blogspot.com/

Hope this helps.

They could work as mutants fighting for the IG, or Orks. I know somebody has a thread called "A squeaky WAAAGH!" or something similar to look to for inspiration.