Verloren/Ayanami has been said to be the 'big bad' of the series from the start, but as the series progressed, hints of another villain being the true culprit behind some of the events in the series began to show up, with the introduction of the shadow man. Right now it would seem that Landkarte/current Katsuragi is the true archvillain, but somehow... I feel like Landkarte was also manipulated as well, especially after the events of manga chapter 92.
I suspect that 1000 years ago, when the Chief of Heaven created Verloren, he (Chief) created someone or something else he wasn't supposed to create. This dark creature then used Verloren's body as a host or a vessel, like one of those parasites in nature that attack and feed off others. Eventually, the dark thing tempted Verloren to reach out and touch Eve, starting the whole long chain of events that have led up to the present.
I have been wondering who or what this dark thing could be, if we assume my theory is correct. And then I thought about opposing qualities and dual natures. Mikhail and Raphael are ideal complements-combat and healing. Some of Verloren's original powers opposed each other e.g. seeing into the past, seeing into the future (which later became Relikt's and Profe's powers when the Seven Ghosts were created), cutting and binding (Zehel's and Fest's powers). That got me thinking that maybe the Chief meant to create an opposite to Eve, and this opposite then became the dark thing/shadow man. And, if it was Eve's opposite....what if it was the Chief's SON?? What if the Chief originally wanted to have two children who complemented each other, like yin and yang, light and darkness?
If so, that would go some way to explain some things. The Chief of Heaven wouldn't want to accuse his son of murdering his daughter, and it would be all too easy to make Verloren the scapegoat. Or it could be that the Chief was in denial. After all, even if he is a god, it can't be easy for a parent to believe that their child is capable of something so terrible. Not only that, I can imagine that kind of storyline happening in 07-Ghost-a son wanting to overthrow his father and gain control of the world, the universe.
While I doubt that my theory will turn out to be correct, I think it would be interesting if it did.