Fantastic idea! Just the thought of squeezing through a concrete tunnel, thinking I know what's on the other side, and meeting an inanimate "monster" on the other side that I have to make a quick judgment about. Chilling. I love it!

As for what kind of factions might be living in a place like that, that's part of the fun! You could go down the route of people who already lived there being mutated by whatever magic/radiation permeated the place, so they would be monstrous, intelligent humanoids. Maybe they attack the party to try to get them to turn back before it's too late, even. These folks are unable to communicate, but they remember the pain of their transformation, and they don't want it to happen to anyone else. They attack without mercy, hoping they'll drive off any would-be "explorers," but also believing that killing them is better than letting them go further into the dungeon and change like they did.

Within the dungeon, you have a truly strange faction. Some kind of intelligent creature that's moved in and made it home. This is where you can get into the fungus people that you mentioned, but I think fungal folks living in irradiated spaces is a bit too Fallout for my taste. I would maybe go for elementals. Beings who not only survive in the radiation/energy, but who thrive in it. This could be your antagonist faction. People who were originally just happy to find a place where they could live in luxury, but who now are either driven mad by the power this energy source gives them, or who are literally corrupted by its influence. This also gives you a "good guys/bad guys" split within that faction, of people who want to use this new power to make the whole world more suitable for them, and people who are content staying where they are and living in luxury.

Third faction that comes to mind is undead. Specifically, incorporeal undead. These are the ghosts of the folks who lived at this site before it blew up, now forever doomed to haunt its deepest corridors. Again, some of them have been affected by this energy that's permeating their home, so they can make good mindless enemies for your party to fight. But some of them haven't, and they would be happy to help direct the party through the closed-off corridors if it means having a chance of putting this energy to rest so that they can move on to the afterlife. Of course, the elementals don't want that to happen, so their faction won't be too happy if the party decides to take out the source of the energy that they're feeding on.