After the surface of the world succumbed to chaos centuries ago, the city of Equestria is kept afloat in the sky solely by the continual prayers offered by the Saint. Years ago, when the Saint's prayer was interrupted, an incident known as the "Forte Maximo" occurred, causing a portion of the land to fall and split the lower city into two, separated by a cliff. Countless lives and property were lost and irreversibly affected in what would be known as the greatest disaster in the city's history.

In time, the lowest layer, known as the "Bastille," became the home to people who lost much of their former lives during the "Forte Maximo." Crime, famine, and disease run rampant, with "The Noncorroding Golden Chain," the ruling organization in the area specializing in the sex trade, keeping what little order that still exists. Meanwhile, a contagious disease which causes the infected to grow wings has spread throughout the city, and a unit commonly known as the "Winged Huntsmen" has been formed to deal with these people swiftly and often violently.

In this "Bastille" resides Rainbow Dash, a freelance ex-assassin who does odd jobs for her friend, the head of "The Noncorroding Golden Chain," for money. During one request, Rainbow Dash finds Fluttershy, a winged girl who emits the pale pink light characteristic of the "Forte Maximo" incident years ago. Her encounter with Fluttershy will take her on a journey which will involve her with the most influential bodies of the city, including the Church and the royal government. As she searches for the meaning to her cruel, difficult life, she will discover the deepest and darkest secrets of Equestria.