Not that you really need to explain zombie/mutant/freak outbreaks in this day and age, but the inclusion of them in Crackdown 2 seems odd. Out of place? Not at all -- these monstrosities tend to mesh nicely with open-world games. Still, there's been little in the way of an explanation so far.
I guess that's where this animated series of videos, "The Pacific City Archives," comes into play. In the attached second episode, they attempt to justify the creatures' existence; for a game like this, I'm willing to believe just about anything and roll with it.
Question is, does any of this stuff reflect the explicit story content for the game, or are these videos merely supplemental? Probably a bit of both.