I'm an aspiring novelist and have run into a literary conundrum that I can't seem to get past...

I've been working on a story for several months now (writing in my free time, which is sparse) and I am having a hard time not making plot/conflict resolutions feel contrived. This is mostly due to the fact that a god is a central idea in the story. So I guess my question is how do you take the "Deus ex Machina" out when the "Deus" is the machine in the first place?