What I disliked at first was how needlessly convoluted it got but then I actually got hooked despite that so props to the mangaka. Now the only thing I really dislike is how gullible the MC is. He jumps from one to the next without really thinking for himself and the only time he tried to think things through on his own it was just panels of panicking.
My theory is that there are multiple girls involved in this case and in the previous incident in middle school. But there is only one tsubasa. I believe it is impossible for there to be multiple tsubasa's because it doesn't make sense for there to be multiple yanderes. That is the hill I will stand on and I will die on it if I must because multiple yanderes for one guy will never work together. But organized crime under one yandere sounds likely and I think this is supported by the different pictures and panels of the different versions of tsubasa we were shown.
Now, although I said there is one tsubasa this doesn't mean there can't be multiple yanderes. There could literally be opposing groups that were put into motion due to the train incident and we have not quite reached an understanding of how many girls actually like MC. And Muira could be in one yandere group (the librarian girls group), and was taken out by the tsubasa group.... Wow, this is one fun rabbit hole of theory I found myself in.