So what's happening is that in this AU, Twilight Sparkle, still feeling guilt and betrayal over her fight with her friends during the events of the MLP movie, feels that she isn't worthy of being the Princess of Friendship anymore, so the night after the Friendship Festival, she sneaks out of her castle and runs away from Ponyville.

Twilight:
I'll run and run all through the night, till I'm far away and free,
and when my energy runs out I'll know, that no one will find me.

But things are not the same as before,
mistakes I make no one can ignore.
I keep my magic performing fine,
I try so hard to keep friendships in line,
but I'm not a useful pony anymore.

I'm not a useful pony anymore...