Core Control Series by Andrew Seiple, Beth Lyons

Wynne might have been human once. It's hard to say. Now he's a bunker core, a nanomachine controller responsible for an entire complex. Of course, the place is a bit wrecked. And the world outside is ruins. And he's pretty sure that whoever put him here is going to come looking for him at some point. And then there's the raiders... Dungeon Core, Post-apocalyptic style. Come for the mutants, stay for the dystopian adventure!

Life can be good when your enemies think you're dead. But Wynne has traded one set of foes for another, and a hunter in oldtech armor wants him for sinister purposes. Neither fully man or machine, it's up to this new bunker core to rise up against all odds, using his wits and technology to prevail against twisted animal-folk, shining mutants, and threats literally from out of this world...