So around 2000-2005, I remember seeing an episode of an anime on tv. I think it was adult swim - I wasn't technically supposed to be watching it. This ninja/fighter goes and slaughters an entire village for some reason. He uses his bare hands somehow, so perhaps he had some special fighting powers.
I believe that he regretted something about it, and afterwards he stands in a river or shore of a lake and starts "slicing" the water to try and clean the blood off of his hands. It's sunset now, and there's more yellow/orange light in the scene. Something tells me that maybe he was wearing a robe of some kind. As he's slashing at the water over and over again, he complains that he "can't get the smell of blood off my hands." That is the part that is most memorable to me.
For a while I've been thinking that it was Inuyasha since that was airing on adult swim in that time period, but it doesn't seem like that show would be that dark. According to my memory the animation style was similar to Princess Mononoke, it was a "serious" show.