Okay, let's toss out a couple of mine:
* Mender Silos has gone back in time to stop/alter the creation of Lord Nemesis (aka: Himself). What he found is that the person everyone believed to be the original Nemesis is in fact just building off of blueprints given to him by someone else, and the guy's DNA doesn't match that of Silos. Unsure of where/when/who the real Nemesis is, Silos is having to make small changes to snowball events into the end he wants, rather than stopping Nemesis directly. And that will lead to his other goals.
* The group that created the 5th Column spun off another group as well. They had a strong interest in magic, and were in league with the Thule Society to investigate it. The Thule Society eventually realized that they didn't believe in a "master" race, but that it was the ability to use/control the forces of magic that marked one as superior. This caused a bitter split that lasts to this day, and left the Council scrounging for pseudo-magical allies such as the Path of the Dark. The Mages of Thule (as they now call themselves) eventually found a pocket dimension in the Atlantic that they decreed the fabled Island of Thule and set up as their base of operations. Due to their concern with magical ability and bloodlines that carry it, they have ties with both the Mu and the Legacy Chain. They actually back the Chain (secretly), and use them as a public front.
* City Hall offers various services and programs to heroes that many don't know about. This includes a small amount of pay for anyone doing enough freelance hero work, therapy sessions, classes on dealing with a crime scene/people before the police arrive, and a wide range of classes that can be summed up as "How to do Basic Stuff That You Never Learned Because Your Dark Backstory Left You With No Life Skills" classes. Most of those classes are taught by heroes that volunteer their time.
* Overbrook has an unusually high population of heroes in the apartments there. That's because the company that owns the apartments felt that offering targeted discounts to heroes would make the building safer than the more hazardous area would suggest.
* There are hero social groups that have formed around having some kinds of powers. Speedsters getting together for morning jogs, flyers playing Quidditch, gun clubs, and so on.