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So in nature, things tend to become more different from wild type (original) with each generation. A "first generation" virus can be as nasty as the wild type, while a second and third generation will tend to mutate away from wild type in response to exposures (plagues??) in their environment.

So what the did Mantic do? They named their big bad plague boss, the thing the least like the human that it came from, as first generation, while the dudes very similar to humans are third generation!

Jeez, did no one give these guys any clue as to how things work in nature? The big guy is the third generation, and the wimpy human-ish grunts are the first generation! Are these guys mutating backwards somehow? Man, what are we gonna get next? A creation science faction?

/stupid pedantic rant done

The plague didn't come from a human source, it comes from alien artefacts that are accidentally unearthed.

So, it makes sense. 1st Gens had direct contact with the alien artefact, 2nd Gens were infected by the 1st Gen, 3rd Gens were infected by 2nd Gens.

Hm. You people who actually read the fluff.

Get off my lawn.

(but ok. that does make a bit more sense...)

The fluff give clues that suggest the plague is actually engineered to work like that. The ideia is to wipe out all life in every planet, using the msot violent and painfull process available. Indeed, the fluff kinda of suggest that the 3rd gen have only one purpose: to learn how, and travel to the next plannet, carring the plague with them.

Carrying 1st and 2nd Gens with them, since the 3rd gens themselves aren't contagious

^but of course Hell, they may even bring the original artifact with them (if it doesn't expend itself creating the first stage 1('s?). )