I saw this 2008/2009. I think it was one of the last episodes but I liked the anime instantly. I remember only the fight scene. The protagonist was tough guy with a blonde hair tied to a ponytail, military sort, wearing round rimmed glasses and was fighting a sort of little girl, in a factory or lab if I remember it right. He was using guns. He thought he killed her but then it turned out she was actually some sort of biological doll or AI or something. Then all of a sudden, there were more of those little girl dolls.
That's all I remember. I've been searching a long time, help would be appreciated.