Tony Stark, when he became Iron Man, realized that SHIELD was blind. Their version of dealing with "new abilities", as they put it, was "ignore them until they become a threat, then recruit". This didn't work, and there was plenty of evidence to prove it. The reason it existed was that, by the time someone was judged a threat, they were desperate enough to accept SHIELD's offer. That didn't sit right with Tony. But what could he, someone with shrapnel lodged in his chest, do?
Quite a lot, actually. Money had power.
Heroes Alliance started up in a refurbished warehouse Tony bought, with a call center for crimes to be discovered (both by cell phone, where HA was simply "444" on any SI phone sold after its inception, and from panic buttons, sold for $10 apiece), an ER, and it's own AI, the Heroes Assistance Manager for Municipal Advice and Defense (HAMMAD). Slowly, heroes trickled in, astonished at a safe haven. At seeing the lack of corruption and shared power at HA, SHIELD employees slowly left to see the new organization. Within months, the four-story building was fully staffed with a rotating cast of heroes, both receiving and giving assistance.
As secrets were revealed, new divisions popped up, including Technical Services; full-time Medical Care, including non-emergency care; Scientific Advancement, which dealt with explaining and creating cures for "conditions"; a therapy office; and RAID, Recognition of Abilities and Intake Division, which focused on powered people who weren't damaged beyond repair. When Sitwell came, he brought a list of children SHIELD was watching, and they started there. HAMMAD scanned headlines every day to see if other people with abilities popped up, and sent his results to RAID. Walking into their office was stark contrast against the cream walls outside; most everything inside RAID was brightly colored, since so many of its users were young.
The best part was that, despite media coverage, HA employed enough regular people (some chosen because they fit certain superheroes' body types) the organization was perfectly anonymous. Fury could never track them down or undermine them effectively, especially as more and more people flocked to them. Of course, some days at HA were far more insane than others…