Personally I have doubts that these concepts are entirely scientifically accurate; however, they are still quite interesting and might serve as inspiration for future game mechanics. Feedback will be sent to ElrodLogan via PM on Discord.
I dunno about having it part of the normal game, but it sounds like a cool special mode, like non-LAWK.
I think the "micro-plague" could continue into the other stages. It'd be a galaxy-wide threat, akin to the Zerg and the Flood, and it'd probably take reaching Ascension to finally defeat. Not just that, but a special God Tool (bonus points if you make it ring-shaped).
Yeah, better leave it out of the main game. Scientifically it doen't make much sense... unless maybe if it is just a virus infection, and not a semi-colony of cells "mutated". Much of the elements you talked about work if it were a virus infection (even the mutation part, as virus infections sometime produce mutations). But I am not very fond of the idea, and definetely not a cancery-colony thingy.
I like the idea; but I agree that it should be some sort of toggleable thing or a mod, rather than actually part of the main game. Because if this does go on to later stages (which would be cool) it would be like playing a completly completely different game. A potentially fun game about trying to either devour the galaxy or a near futile fight to save it, but a different game none the less.