You know, this story is a very enjoyable read, like most of your work, and I wouldn't mind seeing more of it.
That said, I don't actually see the main characters crossing any lines at all.
Mayhaps it is just I, but lines like “I do believe that you begin to understand. I will do nothing to help your friend. Because I will it to be, your Ayame is going to die!” leave us thinking that the Bilwis is a moron who deserves what's coming to her. Lines like that never should be delivered to distraught people, especially not distraught people with weapons and dying friends. It's a rule, like don't mess with old people or the terminally ill and never destroy a collector's collection.
I mean I suppose some people might see a moral grey area here, but it's one that would have made more sense if she was sympathetic. Or perhaps that's me. I do subscribe to the 'if the supervillian makes me choose between a bus full of innocents and my girl friend, save the girlfriend and pretend you didn't see the innocents' school of thought, after all. Now if I had friends on the bus, THEN it'd be a moral dilemma. Not that I'm adverse to saving innocents, I just put strangers on low priority.
Still deliberate inaction is an active threat and pretending otherwise is trying to hide behind semantics, so it's probably not just me. Otherwise you wouldn't need to code against it in Asimov's laws of robotics.
Sorry, got a bit sidetracked there, but it was one of those things where I thought the summary (unless things spiral out from here) was an awkward fit for a good story.

Wow. Nice job! One nit-pick though is that your sentences are to long and complex. (i have the exact same problem) You should try and shorten them. Remember, less is more. Thats what I have to keep telling myself.
I suggest that you go through your story and act as though you just picked it up at the library. Cut out every single thing that would deter you from reading it were it a published novel. That should help. (you would not believe how many visions of my story i went through, and am still going through to this day. I am probably responsible for the destruction of the rainforest considering the number of notebooks I have)

Can't wait to read more!

Good luck,

Ciao!

~nicola~