I am not sure either the story I'm planning right now is a Fantasy story or not.
The setting is a fictional world. Basically, a kind called X (didn't think of a name) comitts genocide against the people living in the land they desire. All the Onyxes are wipped off by the X's. Thing is the Onyxes are magical people, who are able to canalize the powers of the gods they believe in by a stone attached to the skin of the back of their hand when they are young.
The X's realize this and simply cut off their arms before killing them in concentration camps. MC #2 is the only Onyx who escaped (with a arm missing, therefore she can't use her magic), because she wasn't as dependent of her magic.
Fast forwarding to the beginning of the story, all the Onyxes are dead for five years and the weather grows colder. MC #1 is a Doctor who is struggling with the beggining of what seems to be a plague. The Xs believe in a god too, and all MC# 1 does is pray for the sick and clean corpses.
The story is basically MC# 1 and MC# 2 meeting and discovering what is the embryo of science in their world. There are no gods, only the power of the stone the Onyxes used. Somewhere in the story MC #1 receives the power of the Onyxes by carving a stone to his arm, btw.
So it is fantasy because of the stone, right? Even though the story revolves around science?