First, this is an awesome story. Thank you for allowing us into your world. I would have gotten in on this thread earlier but I didn't realize that you were posting the story here. I was following the updates at
http://spiralingstaircase.deviantart.com/
It reminds me favorably of an old SF book I picked up in a used book store some years ago where the female main character was slowly transformed into an alien lizard-like creature. Yours is far more dynamic and engaging.
I love the way The Flesh is portrayed as not evil but simply inhuman. That it has no sense of morality or decency to appeal to, just practicality.
Mary having moments of fun with the whole thing makes the serious moments hit that much harder. Since we are seeing things from her perspective and know what The Body wants we, like Mary, can fail to appreciate how alien and frightening it is for everyone else.
Katie being decidedly *not* OK with the whole part-of-the-collective mentality as well as being Mary's conscience, with the whole kidnapping the nurse turn of events. That being in a tough situation does not excuse you from doing the right thing is both great and realistic. It really grounds the story and draws the reader in.
I also enjoy the way things go from Funny -> Annoying -> Scary so quickly. It has kind of culminated with both Katie reverting while at school and coming to the realization that she can never be more than 3 days away from Mary for the rest of her life. I mean they're friends and all but forever?
As well as the whole subservience thing. No matter how much you know or trust someone you would never give them that kind of power over you. And made doubly scary by Katie's accusation that Mary is no longer acting like the Mary she was only two days ago. She tells Katie that she didn't do it on purpose but how can Katie be sure what Mary is saying is the truth? How can she be sure that this really is Mary at all? As she demonstrated to Katie she is just a bunch of tentacles and when she no longer has a heart, bones or a brain is it really her any longer? Is she really Mary or just a pile of tentacles that looks and sounds like Mary? What was initially funny when Katie called her 'silly putty' has now become very frightening.
Mary is still holding on to the notion that she can somehow be cured when physically there is nothing left of her old form. Despite the facts that when she moves there are no bones involved, when she speaks she isn't using lungs and when she thinks there are no longer a brain or synapses there. I can't wait to see how she reacts when she realizes this. Whether the story ends happily or tragically it will be eagerly read.