I think we need to remember that Lewdlab's previous work, DoD, was over analysed and loads of people, myself included, had guessed the plot long before it had finished and had invented a load of other twists and turns that never happened. The idea that Natsuko is the mastermind is possible i suppose but highly unlikely, IMO she is this game's equivalent to the apparition, popping in to help when needed but otherwise deliberately vague in motive and intent, she could be anything or anyone but IMO she is not a bad guy.
My best guesses currently:
The Father will die/become captured/become a damsel in distress. No matter what he will be put on the bench so that that Connor can get at his mom.
Thorne and the Russian mob are small fish, the father's company and the voice are the main players.
The voice is a character we've already met.
The Halo is a byproduct of the father's company's work, the twin brother discovered it's effects and has been trialling it on his mother and sisters, however things backfired and they went for Connor instead.
The twin brother and the voice are the big bads, no two ways about it, however the voice is female, ergo his girlfriend.
Due to all other male characters being expendable by nature i'm willing to bet that if the father doesn't die then Thorne will, also if Thorne dies it will be shown he isn't as much of a bad guy as he seems.
Both sisters will survive this time, unlikely that Doc Sin will pull that trick twice in a row
Due to lack of plot significance right now the teacher and aunt may in some way be involved with the voice, how i have no idea but if the voice isn't the twins GF then it could be the aunt.
I have no idea what the significance of the MC's female friend is, she could just be an extra girl or threesome fodder but perhaps she is more important, no way to tell yet.