Here's my interpretation. Twilight failed to bring the crystal heart in time to stop King Sombra. He, in turn, succeeded in conquering the crystal empire once more. With his hatred and fear ruling the empire, all of Equestria was covered in darkness.
Te magic of Celestia and luna was not enough, and Sombra vanquished all opposition. Without love, friendship or any other positive magic, the very land began to corrupt and wither away.
And through it all, Twilight, distraught over her failure and the loss of her land and friedns, stays inside her tiny shield, keeping in whatever happy memories she's managed to hold onto through all this. Tears falling down her face, knowing full well that the happy world she knew is gone forever.
A bit bleak I know but that's what came to mind when I saw this picture.
I not like the idea of Celestia and Luna failing, it would mean they send Shinning Armor, Cadence and mane 6 without assisting them on an important world threatening mission without plan B.
Also I still not like Sombra as villain, he should not be Immortal and OP, he is just Unicorn who used power of darkness, he can not be stronger and Alicorns and immortal just because he use power of darkness, because every Unicorn would start using it to get stronger then Celestia and Luna.
I can't give you a story but I can give you a sort of description of the picture. From the looks of the smog/clouds and the trees it seems to me that she is on Earth, and with the size difference between her and the trees it looks to me that she arrived here bigger than one would expect. Also with the emotions she is displaying she is obviously frightened by her new environment and being away from her friends. How she got there could range from being distracted while doing a teleportation spell or Discord getting revenge. I hope that gives you a good idea for a story.
Wow, I think I really have to watch you from now on... First that unique Luna wallpaper and now a sad Twily picture that instantly made me feel tears coming up the very moment I looked at it. Not even Pinkie's Smile Song playing at the EQLA stream on Everfree helps. This picture is just... sad...