It's told backwards. It starts with the carnage and then shows you how it got that way.
The way I see it, the theme seems to be like that line from Nietzsche (sp?) about becoming the thing you hate. The girl hates the Hunters for taking the human lives of her parents, so she takes another human life, her own. And X thinks so much like a human, he makes exactly the same mistake. He's enraged because the girl indiscriminately blamed all Hunters and killed Zero for something he didn't do, so X indiscriminately blames all humans for what she did. That's just my interpretation, though, it may not be what Manatsu-san had in mind.