Yesterday I got the Sigma ending (and I was very surprised because I tought that it was the Luna ending and also that the Sigma ending would have been the "true ending"). It was my sixth ending, and now I got all the secret codes I needed: the two for the lion computer and the four passwords for the bombs. So I think I will now get the three important endings (or at least the true ending when I have to shut down the four bombs plus the other two endings where I have to put the lion passwords). So, I have three main suspects about who Zero Sr. is (please don't spoil me anything):
The first one is Luna. This theory comes from some meta reasonings: the ending where she was the most importsnt character wasn't her ending but Sigma's ending, and she seems the only character that doesn't have any connection to anything or anybody. At the same time, how is it possible that she died in many routes because of Clover (or at least I think it was Clover to "avenge" Alice, maybe the real killer wss Dio or Zero Sr.).
The second suspect is Quark. Similar meta reasoning: I didn't got his ending (the one I thought it was his was the Temyouji one). Also, in̈ a lot of runs where he disappeared people died, so maybe is him: in fact, I think that when Dio says that he hides an evil side he could not be lying.
The third suspect is Phi: yes, it's because I don't get her ending, also because I still don't know anything about her or any connection with anything/anybody. Of course I doubt because she always helps and she is the one with the most brilliant thoughts, but maybe she is a "June-type Zero", so a Zero that has another objective besides killing the partecipants.
This are my theories. Of course they will probably be wrong (I mean... two of them will be 100% wrong if Zero Sr. is a single person) but the only things I'm 100% sure are that Clover, Alice, Dio and Temyouji aren't Zero Sr. (maybe Temyouji helps if Quark is Zero Sr.).
Again, please don't spoil me anything: today I can't play so I will probably finish the game tomorrow. Thank you!
EDIT: if you are interested, in the comment there is a theory regarding K