There are just a few things that I'm confused on in the story.
SPOILERS!!!!!!
1.) If Kasumi was hanging out with Muramasa the entire time, why the hell was one of her clones questioning Helena about Alpha's whereabouts? Unless it was actually Kasumi, but what makes little sense is that Helena sent Kasumi to the rig, and upon finding her there, Hayate and Ayane proceed to kill her. So, the one hounding Helena for Alpha's whereabouts was most likely a clone, right? Why the hell would the clone care?
And 2.) How did Hayate and Ayane know that was a clone? Do they just have magical ninja senses?
I just wish the game was more clear as to what REALLY happened. You're just left with a whole bunch of speculation on why so and so occurred and why he and she did this and that.
Otherwise, I liked the story. Not as cathartic as I would have wished, but a decent story nonetheless. Still, I'm waiting for Jann Lee to die. They could have killed him off in the train! It was the perfect opportunity! *sigh* A chance missed...