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i also like to thing that when Hannibal told Will "i gave you a child" he also meant "i gave you a family" in the way that Hannibal had also been Will's wife
There's something so awfully sinister about the fact that Hannibal was locked up, and content to be so, and didn't try to stir up anything in his time in prison ... until he found out about Molly and Walter. And then he immediately sent someone to kill them. To get rid of them. To destroy this life Will made for himself that did not include Hannibal.
Molly being Will's wife was unacceptable. In fact, Hannibal quite literally couldn't accept it. Whenever he referred to her he always said "the wife". Not "your wife". The wife. Not only is it impersonal and dismissive, it also sounds an awful lot like "the woman you're married to but doesn't hold your heart" sounds an awful lot like "the woman you're married to that can't satisfy you like I can". True homewrecker behaviour Hannibal
And Walter... Walter was just a kid but Hannibal didn't care. Hannibal isn't above killing children, especially this one who dared to fulfil Will's fantasies of being a father that Hannibal felt he had full control and power over. Abigail was conditional on Will behaving (and got taken from Will for his betrayal). Margot's baby had to be gotten rid of because Hannibal hadn't given it to him. Hannibal hadn't given Walter to Will either. He had to be dealt with, just like Margot's baby.
Hannibal is genuinely so awful when he's jealous. We don't see it often - it's usually Will's jealousy that we see (with Alana, Bedelia, Randall etc.) but when Hannibal gets jealous it's terrifying.