This is interesting perspective to SR. Clark not only left Earth without telling Lois, he didn't tell his mom. And when he returned he didn't crash land in Smallville, apparently.
I like the idea of Lois and Martha befriending each other. Does Lois think Clark is Jason's father or Superman? Why is Superman terrified of Lois?
Biggest question for you [Help] is how do you think I should continue beyond this first part? Stick with Lois in the "present" and unravel things as she finds them? Or go back to the beginning with Clark's perspective and lay it all out? I'm honestly undecided between the two. I like the idea of sticking with Lois, but then that means really staying in her point of view without getting into Clark's head at all, and I'm not sure I could resist that temptation
I like the idea of slowly unfolding the mystery through Lois's POV, but since I don't know the mystery. Would you be able to move forward with what's happening with Lois, while moving backwards with what happened to Superman/Clark, starting with how he returned to Earth and ending the story with why he left? Not knowing the details you're planning on presenting us with, I'm just throwing out ideas. Although, I have to admit, my suggestion might be more difficult than the two you presented. I like Mrs. M's suggestion as well.
So far, I already like your story more than the movie. I'm curious what Operation Argus will turn out to be.
Also, when you post your story parts don't forget to check the blue arrow box, which indicates "STORY" to readers.