There are many organizations in the world. These are only a few, and you're welcome to make up more!

The Initiative occupies a compound of regal, classic marble buildings in Kingswood. These buildings are used for publicity events and as housing for heroes. The true HQ is under the compound, in a labyrinthine shelter that's armed and armored. There's ample subterranean space for research facilities, city-wide observation monitors, aircraft and vehicle docks, etc.

The Orion Conglomerate, called Oricon, is a major business conglomerate. It is a high-end producer of electronics (primarily cellphones, tablets, laptops, and computers) and software to rival Microsoft and Apple. It's also the world leader for developing AI and cybernetics. Oricon's HQ is a black glass tower in Innsmouth, and it often recruits from local universities.

Miskatonic University in Innsmouth is a top ten research university with all the bells and whistles. Sentinel Hill Institute of Technology (yes, called SHIT by most, but SenTech officially) is similarly renowned but only teaches science and engineering. Kingsport College is the local public university in Old Town. Dunwich School teaches dance, drama and music, but it's small and selective.

Predating the Initiative, the Freemasons is a secret society that has always included empowered humans and sorcerers. They have some members registered with the Initiative, but many continue to exist in the shadows where they've always been. They keep their association with the Freemasons secret, and they offer support to vigilantes that catch their interest.

Some villains are capable of working with each other for their common benefit. The Alliance is one such sensible organization in Arkham. They are in control of Arkham, and whenever the Initiative has attempted to stop them, the Alliance proved too elusive, too clever, or simply too strong to be captured or killed.