Option1- Let it go into a novel! See where that takes you.
Option 2- In a short story you can't put everything; you can only put the bare minimum that's needed to have the story make sense. I'd take a look at books that tell you how to write short stories. My recommendation: Beginnings, Middles and Ends by Nancy Kress. I've read it, and it helps you work out the kinks in scene structure.
A writer is a world trapped in a person— Victor Hugo
Ink is blood. Paper is bandages. The wounded press books to their heart to know they're not alone.
Maybe try shooting for a novella? Or just write it as a novel. If you're really intent on it being a short story though, then I'd suggest going through your work with a fine-toothed comb and choose what's most important to the story, then cut out all of the excess. You don't need to tell/describe everything that happens, whether it's physical actions, dialog, internal thoughts, etc. Sometimes a lot of feeling and emotion can be be derived from what you DON'T say, rather than what you do.
