Pops was King of the Villa so Bella raped Pops/Leopold because she wanted to have a child but was infertile. However, Noah is not the child of Pops or Lord Heinrich, but seems like he is Sigmund's son because Sigmund raped Bella probably wanting to have her witch powers and most likely the reason why her soul is healess and torn apart. Now, Charlotte's powers have awakened and everything is being revealed but the bishop keeps control over the Lord Heinrich using magic(what kind of magic we still do not know) and is most likely trying to do to Noah(his own son) the same he did to Bella because of his mother's witch powers should be contained within him now.
Hope that clarified your doubts a little and if not well... just read it again xD
I still don't get how this women Bella got pregnant all of sudden if they said that she could not get pregnant and they said Noah is a vessel or something(〜￣△￣)〜 whatttt??? how can she bring an empty thing to the world if it does not have a soal? it...so not making sense.
but thanks anyway for trying to clear it up for me. I still can't believe he is raping HIS OWN SON （/TДT)/ that so wrong in so many levels ヽ(`Д´)ﾉ
I"m soo soo soo confuse by this plot!! what the hell?! ╮(￣▽￣)╭ I don't get what's going on!