There exists a genre involving the protagonist being a dungeon in the style of Dungeon Keeper. Dungeon Keeper Ami is the earliest case I can think of, with I Woke Up As A Dungeon, Now What as the one that reminded me of this particular one. A central conceit of the genre is that the dungeon gains something from fighting adventurers that lets it expand, usually mana, allowing them to create new room types, summon monsters, and cast spells, but is stuck within a certain framework imposed on them.
This particular story was set in a post-apocalyptic setting where the protagonist was an uploaded human mind counseled by an A.I. with the "magic" and creatures being nanomachine swarms. The protagonist's "core" (and I'm pretty sure that was the term used) where he keeps his consciousness stored, which results in him "blacking out" when the system crashes and has to reboot. It also results in the "menu prompts" he accesses looking slightly scrambled. The A.I. counselor is somewhat antagonistic, as the protagonist is too independent. He eventually learns that artificial intelligence tried to wipe out humanity and that the counselor wants him to keep doing that. He just wants to survive, but the human tribes want to wipe him out. At one point, there's an interlude following a set of bestial creations, the result of genetic engineering, and their search for medicine in the ruins of towns.
The protagonist's swarms were vulnerable to fire and water because nanomachines have a lot of surface area individually. Bodies he "ate" turned into black carbon dust as he consumed the other elements in their flesh. He tends off one group of Intruders with a falling elevator, having to trick himself into building it that way because building safety codes are ingrained in his programming. There is another A.I., one of the genocidal ones, who styles his virtual appearance and environment after a Greek god. The protagonist is trying to stay unnoticed, but winds up in confrontation nonetheless.
I think I read it online about 2-3 years ago. It didn't feel like a fanfic, and was not complete at the time, although I think the author also did fanfic, and had published at least one book, and was considering this story for publishing.