@hellica, Starting inwards going out, I would be having my big bad at the biggest building my city with his right-hand lieutenant along with him. the city itself would is then carved up into thirds with a lieutenant in each, each having a personal "army" that kept the area in control in their own ways (have yet to create them so no idea on their themes). Of course, the higher ups are gong to be supers, just not sure on their alignment until the group I will be GMing decides on hero or villain.
Now with the incident, when it started with its widespread death, there was, of course, a real high rise in crime. Looting was commonplace and the more fearful survivors were very afraid for their lives. Most were appearing to be immune to the virus and once the initial downfall of the virus subsided, they reached out and began to rebuild. Problem was that what was supposed to be immunities were actually mutations in some. A few were benign, superficial appearance changes, boosts in intelligence & speed, and the like. But others were wildly obviously changed. Psionic powers, elemental, etc. There were even a smattering of magic users outta the survivors. At the time I will begin my setting, very few will have been born to their powers but there will be those who have, no older than 19, at the oldest.
Mob bosses? I see a few, yea. I think I may have them believe they just "came" up with the idea, most of them. The Older generation, those that initially survived, will recognize them as they are but as younger ones go, they just don't listen and think themselves smart, ya know like normal,
Supercrime? There will be. Even if only a small fraction of the mutations were active, human nature, even mutated humans, aren't perfect. There will be those who will try to take the low road and use their for their own needs. The higher echelons of my Big bad will most certainly be super criminals who got the power if my group goes hero. Maintaining the power through whatever means they want or need.
Climate may be set in the winter which is when I will be starting, I think. There won't be many who will be out but it's actually a perfect time to find scavengers, aggressive but lazy raiders. Some with a mutant gene active.
I won't be making everything my group goes against supers. Better at the start, I think. To get the handle on the situation. I agree with you on Jack Harkness. In fact, I could prolly make a barely viable Jack with my orginal PL of 5. Just need 10 ranks in healing regeneration and the feat diehard.
@Belial & hellica together, Now now, guise, just keep it simple. Just remember that I win always and everything comes together awesomely,