Luna said a few wrong words, and launched the world into Kingdom War One. The Griffins start to attack viciously, and everypony is joining the Equestrian army. Except for the newly crowned Princess Twilight Sparkle. She doesn't fit the requirements of an Equestrian soldier, but a few ponies might have a solution. Twilight receives a potion, and becomes the first Equestrian super soldier. Based on a few parts of the movie, otherwise the plot doesn't follow the movie, the character just represents the hero.

AUTHORS NOTE: The Mane Six do not exist, except for Twilight, as the ending of this will bring them into the next story as the Avengers of Harmony. :)
For all of you who care: (This means Rarity and Spike are the only ones not getting their own story. Sorry about that, I just don't know enough about the Black Widow and Hawkeye. If somebody would like to help with the info, I could make it into a story.)
Captain America: Twilight Sparkle
Iron Man: Rainbow Dash.
Hulk (Because some of you might disagree, the Hulk is quiet and calm, but then unstoppable when angry): Fluttershy
Thor: Applejack
Spiderman (Spiderman was an Avenger in the comics, as I figured this out by word of mouth.): Pinkie Pie
Black Widow: Rarity
Hawkeye: Spike

Loki: Oh dang, you'll have to read Applejack's story once I make it.