From what I remember there was a town full of people that went missing so the military (I think) gets called in. They snoop around and discover it seems like everyone just vanished in the middle of what they were doing. The entity is some huge black mass that travels in the sewers and only comes to feed every few thousand years. If I remember correctly it leaves piles of metal and non organics behind as feces. Any help would be amazing seeing as this is driving me insane.

Dean Koontz wrote a novel like that, "Phantoms." Not sure if it was made into a movie.

Sounds like phantoms with ben affleck and rose mcgowan