Fluttershy was lonely, living in a small house on the edge of Canterlot, and being somewhat reclusive had such an effect. So she decided to find herself a roommate, placing an ad in the paper. To her surprise, it would be answered almost immediately by young Twilight, a witch in training at the academy.

(flutter-Twi, new fav ship, this also might be a bit inspired by Howl's Moving Castle)