It needs more atmosphere.... New to writing I hope this gives you the right inspiration.

oh good it ended on a sweet note

Glad to see this story finally out to the public. Editing this was hard, but fun.

I gotta say, your story is very interesting. I like it. The mystery, the suspense, the sadness. You were not kidding when you said this story was Gore, because the torture scene was incredibly heard to read. Harder to re-read.

You know what would have made this story even better? If you had posted different scenes in different chapters. Made a longer, more suspenseful read. Like this, for instance:

Chapter 1 (Prologue): Applejack finds a sick stranger in her orchard and brings him to the hospital.
Chapter 2: Applejack runs into Twilight, teleport to the hostipal and discuss.
Chapter 3: Twilight tries to have some clothes dated.
Chapter 4: Twilight heads to the Crystal Empire to find out more about the stranger.
Chapter 5: Twilight goes to the hospital and talks to Thomas.
Chapter 6: Flashback scene where Thomas tells Twilight his backstory.
Chapter 7: Twilight frees Thomas.
Chapter 8: Twilight and her friends have read with Thomas, and he become a Ponyville citizen.
Chapter 9 (Epilogue): Fast-forward decades later where Thomas dies in his bed.

I'm not trying to be rude, jlibbey. Just givin' out my suggestions. Writing's hard. I get it. Please don't be mad, because I'm just trying to help.