The freckles concept has been going through a fair degree of evolution in the background of my head. With James Horner's stirring AVATAR soundtrack in the background I think things have finally come together - check this for a brief:
Humanity has been symbiotic partners for the millennia with an organism we call the freckle. These largely dormant hitch-hikers on our DNA are coming to a momentous rebirthing that the Brotherhood sees as a sign of violent cataclysm. For Femto, her freckles have always been a big part of her character, she is even called Femto Freckles at school. When she starts to see her freckles move, at first she thinks she is going crazy, but soon she works out they are forming new patterns. The revelation that these patterns confer her with powers sets in motion a cascade of adventures leading to the showdown with the Brotherhood and the revelation of the destiny of all freckles everywhere.
I already have plot pieces and some descriptive character ideas and more - I just need to narrow all this down to a scriptment of some sort and concept art.