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The space marine drawback have pride in your colors says no models may infiltrate.

Would this apply to allies (say storm troopers)
It would seem that this shouldnt be so but I can see some people arguing for it.

I'd say that strictly, no.

The intent of the rule is that the Chapter is prideful and honorable, and wouldn't even ally themselves with those who skulk and hide.

Besides it's a drawback, it's supposed to suck heh