This situation is less of a 'they were always your father and you just never knew' and more of a 'they basically married your other parent and became your father just to be in a position to control you'.
I swear I've seen this done before...the only instance I can think of, oddly enough, is that episode of the original Powerpuff Girls with Sedusa/Ima Goodlady. ^^;
But anyway...I've been toying with this subplot for a while in a certain script, and since the writing is going so well, and this is exactly the sort of half-nightmarish-half-lowkey-hilarious thing that would fit right in, I'm going to make a serious attempt to use it.
The only problem is that I've never seen much further than the initial insanely awkward and tension-filled confrontation...as fun as that probably will be, if this situation persists, it will likely color the entire latter half of the story, and that's much more important.
I can see them forming a sort of dysfunctional parent-child relationship (MC would have to manage it somehow, in order to keep his mother alive...) and I'm just wondering what interesting things I could do with that.
Some details, if it helps:
-This whole situation is mostly implied...at least the way I imagine it now. Mom and Antagonist aren't actually married; I think the most that will be explicitly told to the reader is that they basically live together, and that she trusts him.
What makes it a little weird (and implies there may be more to this) is that MC's actual father (Mom's actual husband) does exist; he's just unfortunately trapped in another dimension atm (and/or dead...no one really knows yet). So it does look as though she's gotten a 'replacement', so to speak. ^^;
-MC is an amnesiac, who doesn't actually remember Mom. I don't mean to set up that Antagonist could lie to him and make believe they're really related (although that would be SO fun, it would require Mom to also lie to him and she wouldn't do that).
I just mean that MCs reaction to this sitch is a little subdued, compared to what it might be for the average person to watch a known murderer move in on the only family they have left. ^^; He protects her out of his usual heroic obligation, not because he has any special attachment to her.
-In case it's not obvious already, Mom is okay. ^^ She has no idea what's going on, and is just delighted that her long-lost son and her new friend(?) already seem to be well-acquainted.
-What Antagonist wants is to force MC into a kill mission against a bigger threat (bringing their initial conflict back into the story, so MC can't avoid it anymore~). The solution seems like it'd be simple-- why not sacrifice the mad god for your long lost mother-- but (a) by that point, the mad god will be inhabiting the body of MC's friend, who for all intents and purposes is a 9-year-old boy...
...And (b) MC is a bit of a pacifist by nature. I know heroes who 'don't kill' can be annoying, but MC isn't Batman or anything; by then it should be clear to the reader that assassination would be way out of character for him.