After having several friends read through my script and offer some suggestions, I have finished the first re-write of the story.
As it stands, I've removed the clone, and focused more on the relationship between the Commander and M.A.C.U.
I've also added in some narration at the beginning, coming from the Commander, to explain a little more of the back story.
I've also renamed the Commander, as Commander Hudson Brax. It's a much stronger sounding name.
I also started to research his uniform and found a great website that sells some sweet looking overalls. I'm thinking about the grey suit with orange liners, more like the center most colors in the picture with three overalls. These are on http://www.workwearworld.co.uk. I'm going to try to work up a sketch if I have time.
I also added a virus called the Gorvada virus which has crippled almost 90% of the human population.
While Commander Brax is on Kelper 62e, he is searching for a possible cure because it is linked to an enzyme in desert plant life. Kepler 62e is abundant with this type of plant life.
I plan to go through the story one more time before I get someone else to read through it again.