Playing the interview game works pretty well when trying to come up with ideas.
So you have your futuristic fantasy setting and God. Now you need some characters. Is your main character a male or female? How old is he/she? What kind of past does he/she have? What does he/she do in the world? What kind of world does he/she live in? How are things run in the world? Does he/she have any enemies?
Then you can ask questions about the plot. What happens that forces the main character into action? How does he/she react to it? How does this event change the world around him/her? What kinds of people help or hurt the main character as he/she tries to solve the problem?
You also want to ask how God comes into your world. How much are you going to allegorize Him? Are you going to have a character who represents Him, or are you only going to give Him a different name? The best person to ask about this is God Himself. Ask Him to be a part of your writing and He'll show up. The best part is that it'll feel very natural.
Keep asking questions about your characters and your world. Whenever I think about my stories, it's like I'm just watching them in an anime. I kind of just let them go and see how they react to each other and to different events. Then again, I've been writing stories ever since I learned how to write. I suggest watching things, but you might want to set some qualities of your main character to give you something to start with, which leads me to another question: How does your main character see God/whoever represents God? Does this view change as the story goes on? Is it challenged?
So yeah, hammer out the basic gist of your world and your main character. That should give you a good lead into everything else.
Oh! You'll need names for everything! Try
http://www.babynames.com and looking up fantasy name generators if you have trouble coming up with names on your own.