As Miku collects the supplies for Taku she slowly becomes affected by whatever is in the water and plantlife of this area. The implication is that this is the kind of thing that happened to the literally faceless Remnant that you see wandering around the city. They are definitely interested in her and her brother, but not interested in a direct confrontation. You will literally see them run and dive off of buildings rather than interact with her. It makes me wonder if in the original version of this game’s design they were intended to be treated as wandering monsters on the way to collect supplies. Instead they exist as a mysterious but obviously present observing force, like a less creepy version of the G-Man.
By this point I am very convinced that we are heading for a tragic ending. Taku may survive this and leave but I fully expect Miku to spend the rest of her days in this town slowly becoming one of its long-term inhabitants.