do it bro

Something like "A Thousand Splendid Suns" perhaps?

You could maybe start out with a young mare and her family as they struggle to survive the conflict between the three founding factions, windigos, and all the dangerous creatures that inhabit it. (Changelings, manticores, hyrdras, etc)

Then maybe you could follow her daughter, who grows up under the reign of Discord after he takes notice of the attempts at creating order.

She doesn't live to see Equestria's liberation by the Princesses yet is integral to the framework of the resistance movement that protects filly Celestia and Luna after they fall to earth, and the resistance learns about the elements of harmony.

Flash forward to her daughter, who has spent her entire life living in her mother's shadow, as well as basically raising Celestia and Luna on her own, all while constantly on the move searching for the Elements of Harmony (think Sarah Conner). Maybe give them a run in with King Sombra (who has an arrangement with Discord) as they travel. Discord takes notice after Sombra mysteriously disappears.

A desperate race to find the final element (magic) before Discord realizes how much of a threat they are to him. She sacrifices herself to get them the element, and the sisters finally rise up against Discord.

Wow, I totally just wrote all that out.

This sounds like it would be a lot of fun. It would just take a lot of organization first. Like, you'd have to write an outline so you don't get bogged down like some other fanfictions... *cough* fallout equestria *cough*